205 research outputs found

    The number of clone orderings

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    AbstractThis article provides an exponential generating function and a recurrence relation for computing the number of topologically distinct clone orderings.Denote the number of maps for n clones by c(n) and define the exponential generating function C(x)=∑n=0∞c(n)xnn!.We show c(1) = 1, c(2) = 2, c(3) = 10, and, for n > 3, that c(n) = (4n−5)c(n−1)−(4n−7) c(n−2) + (n−2)c(n−3). We show c(n)∼ e3828n(4ne)n We also prove that C(x) = exp (1+ 2x−1−4x)4

    Automatic layout and visualization of biclusters

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    BACKGROUND: Biclustering has emerged as a powerful algorithmic tool for analyzing measurements of gene expression. A number of different methods have emerged for computing biclusters in gene expression data. Many of these algorithms may output a very large number of biclusters with varying degrees of overlap. There are no systematic methods that create a two-dimensional layout of the computed biclusters and display overlaps between them. RESULTS: We develop a novel algorithm for laying out biclusters in a two-dimensional matrix whose rows (respectively, columns) are rows (respectively, columns) of the original dataset. We display each bicluster as a contiguous submatrix in the layout. We allow the layout to have repeated rows and/or columns from the original matrix as required, but we seek a layout of the smallest size. We also develop a web-based search interface for the user to query the genes and samples of interest and visualise the layout of biclusters matching the queries. CONCLUSION: We demonstrate the usefulness of our approach on gene expression data for two types of leukaemia and on protein-DNA binding data for two growth conditions in Saccharomyces cerevisiae. The software implementing the layout algorithm is available at

    Discovering Hierarchical Process Models: an Approach Based on Events Clustering

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    Process mining is a field of computer science that deals with discovery and analysis of process models based on automatically generated event logs. Currently, many companies use this technology for optimization and improving their processes. However, a discovered process model may be too detailed, sophisticated and difficult for experts to understand. In this paper, we consider the problem of discovering a hierarchical business process model from a low-level event log, i.e., the problem of automatic synthesis of more readable and understandable process models based on information stored in event logs of information systems. Discovery of better structured and more readable process models is intensively studied in the frame of process mining research from different perspectives. In this paper, we present an algorithm for discovering hierarchical process models represented as two-level workflow nets. The algorithm is based on predefined event ilustering so that the cluster defines a sub-process corresponding to a high-level transition at the top level of the net. Unlike existing solutions, our algorithm does not impose restrictions on the process control flow and allows for concurrency and iteration

    How Hard Is It to Control an Election by Breaking Ties?

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    We study the computational complexity of controlling the result of an election by breaking ties strategically. This problem is equivalent to the problem of deciding the winner of an election under parallel universes tie-breaking. When the chair of the election is only asked to break ties to choose between one of the co-winners, the problem is trivially easy. However, in multi-round elections, we prove that it can be NP-hard for the chair to compute how to break ties to ensure a given result. Additionally, we show that the form of the tie-breaking function can increase the opportunities for control. Indeed, we prove that it can be NP-hard to control an election by breaking ties even with a two-stage voting rule.Comment: Revised and expanded version including longer proofs and additional result

    Castell: a heterogeneous cmp architecture scalable to hundreds of processors

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    Technology improvements and power constrains have taken multicore architectures to dominate microprocessor designs over uniprocessors. At the same time, accelerator based architectures have shown that heterogeneous multicores are very efficient and can provide high throughput for parallel applications, but with a high-programming effort. We propose Castell a scalable chip multiprocessor architecture that can be programmed as uniprocessors, and provides the high throughput of accelerator-based architectures. Castell relies on task-based programming models that simplify software development. These models use a runtime system that dynamically finds, schedules, and adds hardware-specific features to parallel tasks. One of these features is DMA transfers to overlap computation and data movement, which is known as double buffering. This feature allows applications on Castell to tolerate large memory latencies and lets us design the memory system focusing on memory bandwidth. In addition to provide programmability and the design of the memory system, we have used a hierarchical NoC and added a synchronization module. The NoC design distributes memory traffic efficiently to allow the architecture to scale. The synchronization module is a consequence of the large performance degradation of application for large synchronization latencies. Castell is mainly an architecture framework that enables the definition of domain-specific implementations, fine-tuned to a particular problem or application. So far, Castell has been successfully used to propose heterogeneous multicore architectures for scientific kernels, video decoding (using H.264), and protein sequence alignment (using Smith-Waterman and clustalW). It has also been used to explore a number of architecture optimizations such as enhanced DMA controllers, and architecture support for task-based programming models. ii

    Scalable detection of semantic clones

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    Several techniques have been developed for identifying similar code fragments in programs. These similar fragments, referred to as code clones, can be used to identify redundant code, locate bugs, or gain insight into program design. Existing scalable approaches to clone detection are limited to finding program fragments that are similar only in their contiguous syntax. Other, semantics-based approaches are more resilient to differences in syntax, such as reordered statements, related statements interleaved with other unrelated statements, or the use of semantically equivalent control structures. However, none of these techniques have scaled to real world code bases. These approaches capture semantic information from Program Dependence Graphs (PDGs), program representations that encode data and control dependencies between statements and predicates. Our definition of a code clone is also based on this representation: we consider program fragments with isomorphic PDGs to be clones. In this paper, we present the first scalable clone detection algorithm based on this definition of semantic clones. Our insight is the reduction of the difficult graph similarity problem to a simpler tree similarity problem by mapping carefully selected PDG subgraphs to their related structured syntax. We efficiently solve the tree similarity problem to create a scalable analysis. We have implemented this algorithm in a practical tool and performed evaluations on several million-line open source projects, including the Linux kernel. Compared with previous approaches, our tool locates significantly more clones, which are often more semantically interesting than simple copied and pasted code fragments

    Inferring clonal evolution of tumors from single nucleotide somatic mutations

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    High-throughput sequencing allows the detection and quantification of frequencies of somatic single nucleotide variants (SNV) in heterogeneous tumor cell populations. In some cases, the evolutionary history and population frequency of the subclonal lineages of tumor cells present in the sample can be reconstructed from these SNV frequency measurements. However, automated methods to do this reconstruction are not available and the conditions under which reconstruction is possible have not been described. We describe the conditions under which the evolutionary history can be uniquely reconstructed from SNV frequencies from single or multiple samples from the tumor population and we introduce a new statistical model, PhyloSub, that infers the phylogeny and genotype of the major subclonal lineages represented in the population of cancer cells. It uses a Bayesian nonparametric prior over trees that groups SNVs into major subclonal lineages and automatically estimates the number of lineages and their ancestry. We sample from the joint posterior distribution over trees to identify evolutionary histories and cell population frequencies that have the highest probability of generating the observed SNV frequency data. When multiple phylogenies are consistent with a given set of SNV frequencies, PhyloSub represents the uncertainty in the tumor phylogeny using a partial order plot. Experiments on a simulated dataset and two real datasets comprising tumor samples from acute myeloid leukemia and chronic lymphocytic leukemia patients demonstrate that PhyloSub can infer both linear (or chain) and branching lineages and its inferences are in good agreement with ground truth, where it is available

    A de novo Genome of a Chinese Radish Cultivar

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    AbstractHere, we report a high-quality draft genome of a Chinese radish (Raphanus sativus) cultivar. This draft contains 387.73Mb of assembled scaffolds, 83.93% of the scaffolds were anchored onto nine pseudochromosomes and 95.09% of 43 240 protein-coding genes were functionally annotated. 184.75Mb (47.65%) of repeat sequences was identified in the assembled genome. By comparative analyses of the radish genome against 10 other plant genomes, 2 275 genes in 780 gene families were found unique to R. sativus. This genome is a good reference for genomic study and of great value for genetic improvement of radish

    First Class Copy & Paste

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    The Subtext project seeks to make programming fundamentally easier by altering the nature of programming languages and tools. This paper defines an operational semantics for an essential subset of the Subtext language. It also presents a fresh approach to the problems of mutable state, I/O, and concurrency.Inclusions reify copy & paste edits into persistent relationships that propagate changes from their source into their destination. Inclusions formulate a programming language in which there is no distinction between a programÂs representation and its execution. Like spreadsheets, programs are live executions within a persistent runtime, and programming is direct manipulation of these executions via a graphical user interface. There is no need to encode programs into source text.Mutation of state is effected by the computation of hypothetical recursive variants of the state, which can then be lifted into new versions of the state. Transactional concurrency is based upon queued single-threaded execution. Speculative execution of queued hypotheticals provides concurrency as a semantically transparent implementation optimization

    Decibel: the relational dataset branching system

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    As scientific endeavors and data analysis become increasingly collaborative, there is a need for data management systems that natively support the versioning or branching of datasets to enable concurrent analysis, cleaning, integration, manipulation, or curation of data across teams of individuals. Common practice for sharing and collaborating on datasets involves creating or storing multiple copies of the dataset, one for each stage of analysis, with no provenance information tracking the relationships between these datasets. This results not only in wasted storage, but also makes it challenging to track and integrate modifications made by different users to the same dataset. In this paper, we introduce the Relational Dataset Branching System, Decibel, a new relational storage system with built-in version control designed to address these short-comings. We present our initial design for Decibel and provide a thorough evaluation of three versioned storage engine designs that focus on efficient query processing with minimal storage overhead. We also develop an exhaustive benchmark to enable the rigorous testing of these and future versioned storage engine designs.National Science Foundation (U.S.) (1513972)National Science Foundation (U.S.) (1513407)National Science Foundation (U.S.) (1513443)Intel Science and Technology Center for Big Dat
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