13902125
GCA: A Coclustering Algorithm for Thalamo-Cortico-Thalamic Connectivity Analysis
The reciprocal connectivity between the cerebral cortex and the thalamus in a human brain is involved in consciousness and related to various brain disorders, thus, in-vivo analysis of this connectivity is critically important for brain diagnosis and surgery planning. While existing work either focuses on fiber tracking analysis or on thalamic nuclei segmentation, to our best knowledge, no techniques yet exist for performing in-vivo analysis of thalamo-cortico-thalamic connectivity. In this paper, (i) we propose a new partitioning paradigm, called coclustering, to model this problem. In contrast to the traditional clustering paradigm, a coclustering procedure not only simultaneously partitions cortical voxels and thalamic voxels into groups, but also identifies the corresponding strong connectivities between the two classes of groups; (ii) we develop the first coclustering algorithm, genetic coclustering algorithm (GCA), to solve the coclustering problem; and (iii) we apply GCA to perform in-vivo analysis of the thalamo-cortico-thalamic connectivity and produce a strikingly clear 3D visualization of the seven thalamic nuclei groups as well as their connectivities to the corresponding cortical regions of a human brain
7682350
Incremental genetic K-means algorithm and its application in gene expression data analysis
BackgroundIn recent years, clustering algorithms have been effectively applied in molecular biology for gene expression data analysis. With the help of clustering algorithms such as K-means, hierarchical clustering, SOM, etc, genes are partitioned into groups based on the similarity between their expression profiles. In this way, functionally related genes are identified. As the amount of laboratory data in molecular biology grows exponentially each year due to advanced technologies such as Microarray, new efficient and effective methods for clustering must be developed to process this growing amount of biological data.ResultsIn this paper, we propose a new clustering algorithm, Incremental Genetic K-means Algorithm (IGKA). IGKA is an extension to our previously proposed clustering algorithm, the Fast Genetic K-means Algorithm (FGKA). IGKA outperforms FGKA when the mutation probability is small. The main idea of IGKA is to calculate the objective value Total Within-Cluster Variation (TWCV) and to cluster centroids incrementally whenever the mutation probability is small. IGKA inherits the salient feature of FGKA of always converging to the global optimum. C program is freely available at http://database.cs.wayne.edu/proj/FGKA/index.htm.ConclusionsOur experiments indicate that, while the IGKA algorithm has a convergence pattern similar to FGKA, it has a better time performance when the mutation probability decreases to some point. Finally, we used IGKA to cluster a yeast dataset and found that it increased the enrichment of genes of similar function within the cluster.
6486168
A Dataflow-Oriented Atomicity and Provenance System for Pipelined Scientific Workflows
Scientific workflows have gained great momentum in recent years due to their critical roles in e-Science and cyberinfrastructure applications. However, some tasks of a scientific workflow might fail during execution. A domain scientist might require a region of a scientific workflow to be "atomic". Data provenance, which determines the source data that are used to produce a data item, is also essential to scientific workflows. In this paper, we propose: (i) an architecture for scientific workflow management systems that supports both provenance and atomicity; (ii) a dataflow-oriented atomicity model that supports the notions of commit and abort; and (iii) a dataflow-oriented provenance model that, in addition to supporting existing provenance graphs and queries, also supports queries related to atomicity and failure.
16579446
Mining Correlation between Motifs and Gene Expression
One of the major challenges in the post-genomic era is to determine all DNA-binding transcription factors (TFs) and their regulatory binding sites (motifs) within the genomes. To discover the relationship between the motifs and changes in gene expression, we propose a new algorithm, co-miner (correlation miner). Correlation rules are generated based on the expression profiles of genes with significant expression change through the time course of gene expression. Thus, we may consider the change in gene expression to be causatively associated with the transcription binding sites in the upstream sequences. In addition, we introduce partition and constraint pushing techniques to improve the performance and demonstrate their effectiveness by our experiments. By applying co-miner to a yeast dataset, the relationships between motifs and gene expression revealed by co-miner are confirmed in the literature.
14239575
Semantics based verification and synthesis of BPEL4WS abstract processes
We introduce a logic model to formally specify the semantics of workflows and their composite tasks described as BPEL4WS abstract processes. Based on the model, we present a set of inference rules to deduce the strongest postcondition and weakest precondition of a workflow and demonstrate that automatic workflow verification is possible due to the restrictions on data manipulation in an abstract process. We then sketch an algorithm that automatically synthesizes a workflow given its specification and a task library.
18131628
Automatic workflow verification and generation
Correctness is an important aspect of workflow management systems. However, most of the workflow literature focuses only on the modeling aspects and assumes that a workflow is correct if during the execution it respects the control and data dependency specified by the workflow designer. To address the correctness question properly we propose a new workflow model based on Hoare semantics that allows to: (1) automatically check if the desired outcome of a workflow can be produced by its actual implementation, (2) automatically synthesize a workflow implementation from the workflow specification and a given task library.In particular we: (1) formalize the semantics of workflows and tasks with pre-and postconditions, (2) for each control construct we provide a set of sound inference rules formalizing its semantics. While most of our workflow constructs are standard, two of them are new: the universal and the existential constructs. We then describe algorithms for automatically checking the correctness of workflows and for automatic workflow generation.
896953
Sequential Aggregate Signatures and Multisignatures Without Random Oracles
We present the first aggregate signature, the first multisignature, and the first verifiably encrypted signature provably secure without random oracles. Our constructions derive from a novel application of a recent signature scheme due to Waters. Signatures in our aggregate signature scheme are sequentially constructed, but knowledge of the order in which messages were signed is not necessary for verification. The aggregate signatures obtained are shorter than Lysyanskaya et al. sequential aggregates and can be verified more efficiently than Boneh et al. aggregates. We also consider applications to secure routing and proxy signatures.
13148267
Fair scheduling in wireless packet networks
Fair scheduling of delay and rate-sensitive packet flows over a wireless channel is not addressed effectively by most contemporary wireline fair scheduling algorithms because of two unique characteristics of wireless media: (a) bursty channel errors, and (b) location-dependent channel capacity and errors. Besides, in packet cellular networks, the base station typically performs the task of packet scheduling for both downlink and uplink flows in a cell; however a base station has only a limited knowledge of the arrival processes of uplink flows.In this paper, we propose a new model for wireless fair scheduling based on an adaptation of fluid fair queueing to handle location-dependent error bursts. We describe an ideal wireless fair scheduling algorithm which provides a packetized implementation of the fluid model while assuming full knowledge of the current channel conditions. For this algorithm, we derive the worst-case throughput and delay bounds. Finally, we describe a practical wireless scheduling algorithm which approximates the ideal algorithm. Through simulations, we show that the algorithm achieves the desirable properties identified in the wireless fluid fair queueing model.
1924192
The impact of multihop wireless channel on TCP throughput and loss
This paper studies TCP performance over multihop wireless networks that use the IEEE 802.11 protocol as the access method. Our analysis and simulations show that, given a specific network topology and flow patterns, there exists a TCP window size W*, at which TCP achieves best throughput via improved spatial channel reuse. However, TCP does not operate around W*, and typically grows its average window size much larger; this leads to decreased throughput and increased packet loss. The TCP throughput reduction can be explained by its loss behavior. Our results show that network overload is mainly signified by wireless link contention in multihop wireless networks. As long as the buffer size at each node is reasonably large (say, larger than 10 packets), buffer overflow-induced packet loss is rare and packet drops due to link-layer contention dominate. Link-layer drops offer the first sign for network overload. We further show that multihop wireless links collectively exhibit graceful drop behavior: as the offered load increases, the link contention drop probability also increases, but saturates eventually. In general, the link drop probability is insufficient to stabilize the average TCP window size around W*. Consequently, TCP suffers from reduced throughput due to reduced spatial reuse. We further propose two techniques, link RED and adaptive pacing, through which we are able to improve TCP throughput by 5% to 30% in various simulated topologies. Some simulation results are also validated by real hardware experiments.
3519878
Self-securing ad hoc wireless networks
Mobile ad hoc networking offers convenient infrastructureless communication over the shared wireless channel. However, the nature of ad hoc networks makes them vulnerable to security attacks. Examples of such attacks include passive eavesdropping over the wireless channel, denial of service attacks by malicious nodes and attacks from compromised nodes or stolen devices. Unlike their wired counterpart, infrastructureless ad hoc networks do not have a clear line of defense, and every node must be prepared for encounters with an adversary. Therefore, a centralized or hierarchical network security solution does not work well.This work provides scalable, distributed authentication services in ad hoc networks. Our design takes a self-securing approach, in which multiple nodes (say, k) collaboratively provide authentication services for other nodes in the network. We first formalize a localized trust model that lays the foundation for the design. We further propose refined localized certification services based on our previous work, and develop a new scalable share update to resist more powerful adversaries. Finally, we evaluate the solution through simulation and implementation.
9604157
Conflict resolution in cooperative design
Design is increasingly becoming a cooperative endeavor carried out by multiple agents with diverse kinds of expertise. The development of tools and underlying theories for supporting cooperative design has lagged, however, behind the growing needs implied by this evolution. 
The goal of this thesis work is to provide a computational model for supporting a critical component of cooperative design; the run-time resolution of conflicts. Though the long-term goal is to support unrestricted conflict resolution among human agents, this thesis focuses on an important subset of this problem: the resolution of domain-level conflicts in routine design, using machine-based agents. 
This thesis proposes a model of conflict resolution in cooperative design that corresponds well to how human design experts actually perform cooperative design, based on analysis of their group problem solving activity. This model supports natural participation for human experts, both at development-time as domain experts asked to create machine-based agents, as well as at run-time as problem solving agents themselves. The conflict resolution model is elaborated into a detailed implemented computational theory that offers many insights into how the conflict resolution expert and design agents should operate. The model incorporates a considerable body of conflict resolution expertise applicable to a wide variety of domains, as well as techniques for acquiring further expertise and evaluating its completeness.