11393308
Computational Methods for Analysis of Cryptic Recombination in the Performance of Genomic Recombination Detection Software
The detection of recombination from DNA sequences is relevant to the understanding of evolutionary and molecular genetics. While programs such as GENECONV have been identified as detecting recombination more reliably than others, previous studies have not analyzed how many recombinations they fail to detect. We develop a method for testing how often such programs fail to identify recombinations and how detectability is affected by pairwise differences among the parental sequences. Recombination of sequences having a range of average pairwise differences (APD) is simulated by a stochastic method, and then the history of recombinations is compared to the recombinations identified by GENECONV. With high APD, GENECONV fails to detect ~50% of recombinations; while at a more typical intraspecies APD of 1% to 2%, >70% of recombinations are undetected. Quantitative results suggest corrections for estimating recombination rates more accurately and methods to detect evidence of recombination more consistently.
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.
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.
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.
1137858
Runtime Security Verification for Itinerary-Driven Mobile Agents
We present a new approach to ensure the secure execution of itinerary-driven mobile agents, in which the specification of the navigational behavior of an agent is separated from the specification of its computational behavior. We empower each host with an access control policy so that the host will deny the access from an agent whose itinerary does not conform to the host's access control policy. A host uses model checking algorithms to check if the itinerary of the agent conforms to its access control policy written in mu-calculus, and if so, grant access permission. In order to address the state explosion problem for model checking itineraries, we propose an approach called model generation code. In this approach, instead of verifying the itinerary itself, a host actually checks the conservative models of a mobile agent. If a conservative model does not satisfy the host's access control policy, the mobile agent will provide refined models for further verification. Our preliminary results show that this is a practical and promising approach to ensure the secure execution of mobile agents
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.
6309018
Knowledge-based learning integrating acquisition and learning
Empirical learning algorithms are hampered by their inability to use domain knowledge to guide the induction of new rules. This paper describes knowledge-based learning, an approach to learning that selects the examples and relevant attributes for an empirical algorithm. Knowledge-based learning can be used for developing rules for engineering expert systems. Engineers often have some rules for problem solving, but also many experiences (examples) that facilitate solving problems. Knowledge-based learning systems are able to use both forms of knowledge.
33554044
PEAS: a robust energy conserving protocol for long-lived sensor networks
In this paper we present PEAS, a robust energy-conserving protocol that can build long-lived, resilient sensor networks using a very large number of small sensors with short battery lifetime. PEAS extends the network lifetime by maintaining a necessary set of working nodes and turning off redundant ones. PEAS operations are based on individual node's observation of the local environment and do not require any node to maintain per neighbor node state. PEAS performance possesses a high degree of robustness in the presence of both node power depletions and unexpected failures. Our simulations and analysis show that PEAS can maintain an adequate working node density in the face of up to 38% node failures, and it can maintain roughly a constant overhead level under various deployment conditions ranging from sparse to very dense node deployment by using less than 1% of total energy consumption. As a result, PEAS can extend a sensor network's functioning time in linear proportion to the deployed sensor population.
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.
12858200
Building Robust Learning Systems by Combining Induction and Optimization
Each concept description language and search strategy has an inherent inductive bias, a preference for some hypotheses over others. No single inductive bias performs optimally on all problems. This paper describes a system that couples induction with optimization to carry out an efficient search of large regions of inductive bias space. Experimental results are reported demonstrating the system's capacity to choose optimal biases even for complex and noisy problems.
18477384
Verifiable Shuffle of Large Size Ciphertexts
A shuffle is a permutation and rerandomization of a set of ciphertexts. Among other things, it can be used to construct mix-nets that are used in anonymization protocols and voting schemes. While shuffling is easy, it is hard for an outsider to verify that a shuffle has been performed correctly. We suggest two efficient honest verifier zero-knowledge (HVZK) arguments for correctness of a shuffle. Our goal is to minimize round-complexity and at the same time have low communicational and computational complexity. 
 
The two schemes we suggest are both 3-move HVZK arguments for correctness of a shuffle. We first suggest a HVZK argument based on homomorphic integer commitments, and improve both on round complexity, communication complexity and computational complexity in comparison with state of the art. The second HVZK argument is based on homomorphic commitments over finite fields. Here we improve on the computational complexity and communication complexity when shuffling large ciphertexts.