ALBERT

Description: In the classic k -center problem, we are given a metric graph, and the objective is to select k nodes as centers such that the maximum distance from any vertex to its closest center is minimized. In this paper, we consider two important generalizations of k -center, the matroid center problem and the knapsack center problem. Both problems are motivated by recent content distribution network applications. Our contributions can be summarized as follows: (1) We consider the matroid center problem in which the centers are required to form an independent set of a given matroid. We show this problem is NP-hard even on a line. We present a 3-approximation algorithm for the problem on general metrics. We also consider the outlier version of the problem where a given number of vertices can be excluded as outliers from the solution. We present a 7-approximation for the outlier version. (2) We consider the (multi-)knapsack center problem in which the centers are required to satisfy one (or more) knapsack constraint(s). It is known that the knapsack center problem with a single knapsack constraint admits a 3-approximation. However, when there are at least two knapsack constraints, we show this problem is not approximable at all. To complement the hardness result, we present a polynomial time algorithm that gives a 3-approximate solution such that one knapsack constraint is satisfied and the others may be violated by at most a factor of \(1+\epsilon \) . We also obtain a 3-approximation for the outlier version that may violate the knapsack constraint by \(1+\epsilon \) .

Description: We design a succinct data structure for representing a poset that, given two elements, can report whether one precedes the other in constant time. This is equivalent to succinctly representing the transitive closure graph of the poset, and we note that the same method can also be used to succinctly represent the transitive reduction graph. For an n element poset, the data structure occupies \(n^2/4 + o(n^2)\) bits in the worst case. Furthermore, a slight extension to this data structure yields a succinct oracle for reachability in arbitrary directed graphs. Thus, using no more than a quarter of the space required to represent an arbitrary directed graph, reachability queries can be supported in constant time. We also consider the operation of listing all the successors or predecessors of a given element, and show how to do this in constant time per element reported using a slightly modified version of our succinct data structure.

Description: We consider a graph observability problem: how many edge colors are needed for an unlabeled graph so that an agent, walking from node to node, can uniquely determine its location from just the observed color sequence of the walk? Specifically, let G ( n ,  d ) be an edge-colored subgraph of d -dimensional (directed or undirected) lattice of size \(n^d = n \times n \times \cdots \times n\) . We say that G ( n ,  d ) is t -observable if an agent can uniquely determine its current position in the graph from the color sequence of any t -dimensional walk, where the dimension is the number of different directions spanned by the edges of the walk. A walk in an undirected lattice G ( n ,  d ) has dimension between 1 and d , but a directed walk can have dimension between 1 and 2 d because of two different orientations for each axis. We derive bounds on the number of colors needed for t -observability. Our main result is that \(\varTheta (n^{d/t})\) colors are both necessary and sufficient for t -observability of G ( n ,  d ), where d is considered a constant. This shows an interesting dependence of graph observability on the ratio between the dimension of the lattice and that of the walk. In particular, the number of colors for full-dimensional walks is \(\varTheta (n^{1/2})\) in the directed case, and \(\varTheta (n)\) in the undirected case, independent of the lattice dimension. All of our results extend easily to non-square lattices: given a lattice graph of size \(N = n_1 \times n_2 \times \cdots \times n_d\) , the number of colors for t -observability is \(\varTheta (\root t \of {N})\) .

Description: We revisit the matrix problems sparse null space and matrix sparsification , and show that they are equivalent. We then proceed to seek algorithms for these problems: we prove the hardness of approximation of these problems, and also give a powerful tool to extend algorithms and heuristics for sparse approximation theory to these problems.

Description: We introduce Planar Disjoint Paths Completion , a completion counterpart of the Disjoint Paths problem, and study its parameterized complexity. The problem can be stated as follows: given a, not necessarily connected, plane graph G ,  k pairs of terminals, and a face F of G ,  find a minimum-size set of edges, if one exists, to be added inside F so that the embedding remains planar and the pairs become connected by k disjoint paths in the augmented network. Our results are twofold: first, we give an upper bound on the number of necessary additional edges when a solution exists. This bound is a function of k , independent of the size of G . Second, we show that the problem is fixed-parameter tractable, in particular, it can be solved in time \(f(k)\cdot n^{2}\) .

Description: Digital circuits are expected to increasingly suffer from more hard faults due to technology scaling. Especially, a single hard fault in ALU (Arithmetic Logic Unit) might lead to a total failure in processors or significantly reduce their performance. To address these increasingly important problems, we propose a novel cost-efficient fault-tolerant mechanism for the ALU, called LIZARD. LIZARD employs two half-word ALUs, instead of a single full-word ALU, to perform computations with concurrent fault detection. When a fault is detected, the two ALUs are partitioned into four quarter-word ALUs. After diagnosing and isolating a faulty quarter-word ALU, LIZARD continues its operation using the remaining ones, which can detect and isolate another fault. Even though LIZARD uses narrow ALUs for computations, it adds negligible performance overhead through exploiting predictability of the results in the arithmetic computations. We also present the architectural modifications when employing LIZARD for scalar as well as superscalar processors. Through comparative evaluation, we demonstrate that LIZARD outperforms other competitive fault-tolerant mechanisms in terms of area, energy consumption, performance and reliability.

Description: Information searches are the most common application within social networks. Normally, the social network is modeled as a network graph, consisting of nodes (In the rest of the paper, unless otherwise specified, we will use the terms “user” and “node” interchangeably.) representing users within the network and edges representing relationships between users. Choosing the appropriate nodes to form an auxiliary structure for supporting the effective query message spreading can reduce the troublesome repeated queries. To accomplish this, a hybrid search (HS) scheme is proposed. If the query message is received by a node belonging the auxiliary structure constructed by dynamic weighted distributed label clustering (DW-DLC), it would be flooded to all neighbors of the visited node; otherwise, it would be forwarded to one neighbor of the visited node. The DW-DLC based auxiliary structure can accelerate the process of obtaining required information within the network. The simulation results show that the HS+DW-DLC scheme can reduce the average searching delay time, even in a required-information-scarce social network. In addition, the proposed scheme can generate a relatively low amount of repeated messages to lower repeatedly asking social network users.

Description: This paper presents a derivation of four radix-2 division algorithms by digit recurrence. Each division algorithm selects a quotient digit from the over-redundant digit set {−2, −1, 0, 1, 2}, and the selection of each quotient digit depends only on the two most-significant digits of the partial remainder in a redundant representation. Two algorithms use a two’s complement representation for the partial remainder and carry-save additions, and the other two algorithms use a binary signed-digit representation for the partial remainder and carry-free additions. Three algorithms are novel. The fourth algorithm has been presented before. Results from the synthesized netlists show that two of our fastest algorithms achieve an improvement of 10 percent in latency per iteration over a standard radix-2 SRT algorithm at the cost of 36 percent more power and 50 percent more area.

Description: We present WaFS, a user-level file system, and a related scheduling algorithm for scientific workflow computation in the cloud. WaFS’s primary design goal is to automatically detect and gather the explicit and implicit data dependencies between workflow jobs, rather than high-performance file access. Using WaFS’s data, a workflow scheduler can either make effective cost-performance tradeoffs or improve storage utilization. Proper resource provisioning and storage utilization on pay-as-you-go clouds can be more cost effective than the uses of resources in traditional HPC systems. WaFS and the scheduler controls the number of concurrent workflow instances at runtime so that the storage is well used, while the total makespan (i.e., turnaround time for a workload) is not severely compromised. We describe the design and implementation of WaFS and the new workflow scheduling algorithm based on our previous work. We present empirical evidence of the acceptable overheads of our prototype WaFS and describe a simulation-based study, using representative workflows, to show the makespan benefits of our WaFS-enabled scheduling algorithm.

Description: This paper presents an anomaly detection model that is granular and distributed to accurately and efficiently identify sensed data anomalies within wireless sensor networks. A more decentralised mechanism is introduced with wider use of in-network processing on a hierarchical sensor node topology resulting in a robust framework for dynamic data domains. This efficiently addresses the big data issue that is encountered in large scale industrial sensor network applications. Data vectors on each node’s observation domain is first partitioned using an unsupervised approach that is adaptive regarding dynamic data streams using cumulative point-wise entropy and average relative density . Second order statistical analysis applied on average relative densities and mean entropy values is then used to differentiate anomalies through robust and adaptive thresholds that are responsive to a dynamic environment. Anomaly detection is then performed in a non-parametric and non-probabilistic manner over the different network tiers in the hierarchical topology in offering increased granularity for evaluation. Experiments were performed extensively using both real and artificial data distributions representative of different dynamic and multi-density observation domains. Results demonstrate higher accuracies in detection as more than 94 percent accompanied by a desirable reduction of more than 85 percent in communication costs when compared to existing centralized methods.

Description: This study proposes a quantitative measurement of split of the second heart sound (S2) based on nonstationary signal decomposition to deal with overlaps and energy modeling of the subcomponents of S2. The second heart sound includes aortic (A2) and pulmonic (P2) closure sounds. However, the split detection is obscured due to A2-P2 overlap and low energy of P2. To identify such split, HVD method is used to decompose the S2 into a number of components while preserving the phase information. Further, A2s and P2s are localized using smoothed pseudo Wigner-Ville distribution followed by reassignment method. Finally, the split iscalculated by taking the differences between the means of time indices of A2s and P2s. Experiments on total 33 clips of S2 signals are performed for evaluation of the method. The mean ± standard deviation of the split is 34.7 ± 4.6 ms. The method measures the splitefficiently, even when A2-P2 overlap is ≤ 20 ms and the normalized peak temporal ratio of P2 to A2 is low (≥ 0.22). This proposed method thus, demonstrates its robustness by defining split detectability (SDT), the split detection aptness through detecting P2s, by measuring upto 96 percent. Such findings reveal the effectiveness of the method as competent against the other baselines, especially for A2-P2 overlaps and low energy P2.

Description: Post-acquisition denoising of magnetic resonance (MR) images is an important step to improve any quantitative measurement of the acquired data. In this paper, assuming a Rician noise model, a new filtering method based on the linear minimum mean square error (LMMSE) estimation is introduced, which employs the self-similarity property of the MR data to restore the noise-less signal. This method takes into account the structural characteristics of images and the Bayesian mean square error (Bmse) of the estimator to address the denoising problem. In general, a twofold data processing approach is developed; first, the noisy MR data is processed using a patch-based L 2 -norm similarity measure to provide the primary set of samples required for the estimation process. Afterwards, the Bmse of the estimator is derived as the optimization function to analyze the pre-selected samples and minimize the error between the estimated and the underlying signal. Compared to the LMMSE method and also its recently proposed SNR-adapted realization (SNLMMSE), the optimized way of choosing the samples together with the automatic adjustment of the filtering parameters lead to a more robust estimation performance with our approach. Experimental results show the competitive performance of the proposed method in comparison with related state-of-the-art methods.

Description: Large-scale ad hoc analytics of genomic data is popular using the R-programming language supported by over 700 software packages provided by Bioconductor. More recently, analytical jobs are benefitting from on-demand computing and storage, their scalability and their low maintenance cost, all of which are offered by the cloud. While biologists and bioinformaticists can take an analytical job and execute it on their personal workstations, it remains challenging to seamlessly execute the job on the cloud infrastructure without extensive knowledge of the cloud dashboard. How analytical jobs can not only with minimum effort be executed on the cloud, but also how both the resources and data required by the job can be managed is explored in this paper. An open-source light-weight framework for executing R-scripts using Bioconductor packages, referred to as ‘RBioCloud’, is designed and developed. RBioCloud offers a set of simple command-line tools for managing the cloud resources, the data and the execution of the job. Three biological test cases validate the feasibility of RBioCloud. The framework is available from http://www.rbiocloud.com .

Description: Of major interest to translational genomics is the intervention in gene regulatory networks (GRNs) to affect cell behavior; in particular, to alter pathological phenotypes. Owing to the complexity of GRNs, accurate network inference is practically challenging and GRN models often contain considerable amounts of uncertainty. Considering the cost and time required for conducting biological experiments, it is desirable to have a systematic method for prioritizing potential experiments so that an experiment can be chosen to optimally reduce network uncertainty. Moreover, from a translational perspective it is crucial that GRN uncertainty be quantified and reduced in a manner that pertains to the operational cost that it induces, such as the cost of network intervention. In this work, we utilize the concept of mean objective cost of uncertainty (MOCU) to propose a novel framework for optimal experimental design. In the proposed framework, potential experiments are prioritized based on the MOCU expected to remain after conducting the experiment. Based on this prioritization, one can select an optimal experiment with the largest potential to reduce the pertinent uncertainty present in the current network model. We demonstrate the effectiveness of the proposed method via extensive simulations based on synthetic and real gene regulatory networks.

Description: A novel approach to Contact Map Overlap (CMO) problem is proposed using the two dimensional clusters present in the contact maps. Each protein is represented as a set of the non-trivial clusters of contacts extracted from its contact map. The approach involves finding matching regions between the two contact maps using approximate 2D-pattern matching algorithm and dynamic programming technique. These matched pairs of small contact maps are submitted in parallel to a fast heuristic CMO algorithm. The approach facilitates parallelization at this level since all the pairs of contact maps can be submitted to the algorithm in parallel. Then, a merge algorithm is used in order to obtain the overall alignment. As a proof of concept, MSVNS, a heuristic CMO algorithm is used for global as well as local alignment. The divide and conquer approach is evaluated for two benchmark data sets that of Skolnick and Ding et al. It is interesting to note that along with achieving saving of time, better overlap is also obtained for certain protein folds.

Description: Canalizing genes possess broad regulatory power over a wide swath of regulatory processes. On the other hand, it has been hypothesized that the phenomenon of intrinsically multivariate prediction (IMP) is associated with canalization. However, applications have relied on user-selectable thresholds on the IMP score to decide on the presence of IMP. A methodology is developed here that avoids arbitrary thresholds, by providing a statistical test for the IMP score. In addition, the proposed procedure allows the incorporation of prior knowledge if available, which can alleviate the problem of loss of power due to small sample sizes. The issue of multiplicity of tests is addressed by family-wise error rate (FWER) and false discovery rate (FDR) controlling approaches. The proposed methodology is demonstrated by experiments using synthetic and real gene-expression data from studies on melanoma and ionizing radiation (IR) responsive genes. The results with the real data identified DUSP1 and p53, two well-known canalizing genes associated with melanoma and IR response, respectively, as the genes with a clear majority of IMP predictor pairs. This validates the potential of the proposed methodology as a tool for discovery of canalizing genes from binary gene-expression data. The procedure is made available through an R package.

Description: We prove that in a graph with n vertices, induced chordal and interval subgraphs with the maximum number of vertices can be found in time \(\mathcal {O}(2^{\lambda n})\) for some \(\lambda 〈1\) . These are the first algorithms breaking the trivial \(2^n n^{\mathcal {O}(1)}\) bound of the brute-force search for these problems.

Description: We investigate the effect of limiting the number of reserve prices on the revenue in a probabilistic single item auction. In the model considered, bidders compete for an impression drawn from a known distribution of possible types. The auction mechanism sets up to \(\ell \) reserve prices, and each impression type is assigned the highest reserve price lower than the valuation of some bidder for it. The bidder proposing the highest bid for an arriving impression gets it provided his bid is at least the corresponding reserve price, and pays the maximum between the reserve price and the second highest bid. Since the number of impression types may be huge, we consider the revenue \(R_{\ell }\) that can be ensured using only \(\ell \) reserve prices. Our main results are tight lower bounds on \(R_{\ell }\) for the cases where the impressions are drawn from the uniform or a general probability distribution.

Description: The Regression Network plugin for Cytoscape ( RegNetC ) implements the RegNet algorithm for the inference of transcriptional association network from gene expression profiles. This algorithm is a model tree-based method to detect the relationship between each gene and the remaining genes simultaneously instead of analyzing individually each pair of genes as correlation-based methods do. Model trees are a very useful technique to estimate the gene expression value by regression models and favours localized similarities over more global similarity, which is one of the major drawbacks of correlation-based methods. Here, we present an integrated software suite, named RegNetC , as a Cytoscape plugin that can operate on its own as well. RegNetC facilitates, according to user-defined parameters, the resulted transcriptional gene association network in .sif format for visualization, analysis and interoperates with other Cytoscape plugins, which can be exported for publication figures. In addition to the network, the RegNetC plugin also provides the quantitative relationships between genes expression values of those genes involved in the inferred network, i.e., those defined by the regression models.

Description: The problem of securing data present on USB memories and SD cards has not been adequately addressed in the cryptography literature. While the formal notion of a tweakable enciphering scheme (TES) is well accepted as the proper primitive for secure data storage, the real challenge is to design a low cost TES which can perform at the data rates of the targeted memory devices. In this work, we provide the first answer to this problem. Our solution, called STES, combines a stream cipher with a XOR universal hash function. The security of STES is rigorously analyzed in the usual manner of provable security approach. By carefully defining appropriate variants of the multi-linear hash function and the pseudo-dot product based hash function we obtain controllable trade-offs between area and throughput. We combine the hash function with the recent hardware oriented stream ciphers, namely Mickey, Grain and Trivium. Our implementations are targeted towards two low cost FPGAs—Xilinx Spartan 3 and Lattice ICE40. Simulation results demonstrate that the speeds of encryption/decryption match the data rates of different USB and SD memories. We believe that our work opens up the possibility of actually putting FPGAs within controllers of such memories to perform low-level in-place encryption.

Description: Cellular automata (CAs) have been widely used to model and simulate physical systems and processes. CAs have also been successfully used as a VLSI architecture that proved to be very efficient at least in terms of silicon-area utilization and clock-speed maximization. Quantum cellular automata (QCAs) as one of the promising emerging technologies for nanoscale and quantum computing circuit implementation, provides very high scale integration, very high switching frequency and extremely low power characteristics. In this paper we present a new automated design architecture and a tool, namely DATICAQ (Design Automation Tool of 1-D CAs using QCAs), that builds a bridge between 1-D CAs as models of physical systems and processes and 1-D QCAs as nanoelectronic architecture. The QCA implementation of CAs not only drives the already developed CAs circuits to the nanoelectronics era but improves their performance significantly. The inputs of the proposed architecture are CA dimensionality, size, local rule, and initial and boundary conditions imposed by the particular problem. DATICAQ produces as output the layout of the QCA implementation of the particular 1-D CA model. Simulations of CA models for zero and periodic boundary conditions and the corresponding QCA circuits showed that the CA models have been successfully implemented.

Description: Role-based access control is an important access control method for securing computer systems. A role-based access control policy can be implemented incorrectly due to various reasons, such as programming errors. Defects in the implementation may lead to unauthorized access and security breaches. To reveal access control defects, this paper presents a model-based approach to automated generation of executable access control tests using predicate/transition nets. Role-permission test models are built by integrating declarative access control rules with functional test models or contracts (preconditions and postconditions) of the associated activities (the system functions). The access control tests are generated automatically from the test models to exercise the interactions of access control activities. They are transformed into executable code through a model-implementation mapping that maps the modeling elements to implementation constructs. The approach has been implemented in an industry-adopted test automation framework that supports the generation of test code in a variety of languages. The full model-based testing process has been applied to three systems implemented in Java. The effectiveness is evaluated through mutation analysis of role-based access control rules. The experiments show that the model-based approach is highly effective in detecting the seeded access control defects.

Description: Heterogeneous multiprocessor systems, which are composed of a mix of processing elements, such as commodity multicore processors, graphics processing units (GPUs), and others, have been widely used in scientific computing community. Software applications incorporate the code designed and optimized for different types of processing elements in order to exploit the computing power of such heterogeneous computing systems. In this paper, we consider the problem of optimal distribution of the workload of data-parallel scientific applications between processing elements of such heterogeneous computing systems. We present a solution that uses functional performance models (FPMs) of processing elements and FPM-based data partitioning algorithms. Efficiency of this approach is demonstrated by experiments with parallel matrix multiplication and numerical simulation of lid-driven cavity flow on hybrid servers and clusters.

Description: In this paper, we propose a new notion called $k$ -times attribute-based anonymous access control , which is particularly designed for supporting cloud computing environment. In this new notion, a user can authenticate himself/herself to the cloud computing server anonymously. The server only knows the user acquires some required attributes, yet it does not know the identity of this user. In addition, we provide a $k$ -times limit for anonymous access control. That is, the server may limit a particular set of users (i.e., those users with the same set of attribute) to access the system for a maximum $k$ -times within a period or an event. Further additional access will be denied. We also prove the security of our instantiation. Our implementation result shows that our scheme is practical.

Description: In face of high partial and complete disk failure rates and untimely system crashes, the executions of low-priority background tasks become increasingly frequent in large-scale data centers. However, the existing algorithms are all reactive optimizations and only exploit the temporal locality of workloads to reduce the user I/O requests during the low-priority background tasks. To address the problem, this paper proposes Intelligent Data Outsourcing (IDO), a zone-based and proactive data migration optimization, to significantly improve the efficiency of the low-priority background tasks. The main idea of IDO is to proactively identify the hot data zones of RAID-structured storage systems in the normal operational state. By leveraging the prediction tools to identify the upcoming events, IDO proactively migrates the data blocks belonging to the hot data zones on the degraded device to a surrogate RAID set in the large-scale data centers. Upon a disk failure or crash reboot, most user I/O requests addressed to the degraded RAID set can be serviced directly by the surrogate RAID set rather than the much slower degraded RAID set. Consequently, the performance of the background tasks and user I/O performance during the background tasks are improved simultaneously. Our lightweight prototype implementation of IDO and extensive trace-driven experiments on two case studies demonstrate that, compared with the existing state-of-the-art approaches, IDO effectively improves the performance of the low-priority background tasks. Moreover, IDO is portable and can be easily incorporated into any existing algorithms for RAID-structured storage systems.

Description: Cloud computing that provides elastic computing and storage resource on demand has become increasingly important due to the emergence of “big data”. Cloud computing resources are a natural fit for processing big data streams as they allow big data application to run at a scale which is required for handling its complexities (data volume, variety and velocity). With the data no longer under users’ direct control, data security in cloud computing is becoming one of the most concerns in the adoption of cloud computing resources. In order to improve data reliability and availability, storing multiple replicas along with original datasets is a common strategy for cloud service providers. Public data auditing schemes allow users to verify their outsourced data storage without having to retrieve the whole dataset. However, existing data auditing techniques suffers from efficiency and security problems. First, for dynamic datasets with multiple replicas, the communication overhead for update verifications is very large, because each update requires updating of all replicas, where verification for each update requires O(log n ) communication complexity. Second, existing schemes cannot provide public auditing and authentication of block indices at the same time. Without authentication of block indices, the server can build a valid proof based on data blocks other than the blocks client requested to verify. In order to address these problems, in this paper, we present a novel public auditing scheme named MuR-DPA. The new scheme incorporated a novel authenticated data structure (ADS) based on the Merkle hash tree (MHT), which we call MR-MHT. To support full dynamic data updates and authentication of block indices, we included rank and level values in computation of MHT nodes. In contrast to existing schemes, level values of nodes in MR-MHT are assigned in a top-down order, and all replica blocks for each data block are organized into a - ame replica sub-tree. Such a configuration allows efficient verification of updates for multiple replicas. Compared to existing integrity verification and public auditing schemes, theoretical analysis and experimental results show that the proposed MuR-DPA scheme can not only incur much less communication overhead for both update verification and integrity verification of cloud datasets with multiple replicas, but also provide enhanced security against dishonest cloud service providers.

Description: We introduce a new method for normalization of data acquired by liquid chromatography coupled with mass spectrometry (LC-MS) in label-free differential expression analysis. Normalization of LC-MS data is desired prior to subsequent statistical analysis to adjust variabilities in ion intensities that are not caused by biological differences but experimental bias. There are different sources of bias including variabilities during sample collection and sample storage, poor experimental design, noise, etc. In addition, instrument variability in experiments involving a large number of LC-MS runs leads to a significant drift in intensity measurements. Although various methods have been proposed for normalization of LC-MS data, there is no universally applicable approach. In this paper, we propose a Bayesian normalization model (BNM) that utilizes scan-level information from LC-MS data. Specifically, the proposed method uses peak shapes to model the scan-level data acquired from extracted ion chromatograms (EIC) with parameters considered as a linear mixed effects model. We extended the model into BNM with drift (BNMD) to compensate for the variability in intensity measurements due to long LC-MS runs. We evaluated the performance of our method using synthetic and experimental data. In comparison with several existing methods, the proposed BNM and BNMD yielded significant improvement.

Description: Performing clustering analysis is one of the important research topics in cancer discovery using gene expression profiles, which is crucial in facilitating the successful diagnosis and treatment of cancer. While there are quite a number of research works which perform tumor clustering, few of them considers how to incorporate fuzzy theory together with an optimization process into a consensus clustering framework to improve the performance of clustering analysis. In this paper, we first propose a random double clustering based cluster ensemble framework (RDCCE) to perform tumor clustering based on gene expression data. Specifically, RDCCE generates a set of representative features using a randomly selected clustering algorithm in the ensemble, and then assigns samples to their corresponding clusters based on the grouping results. In addition, we also introduce the random double clustering based fuzzy cluster ensemble framework (RDCFCE), which is designed to improve the performance of RDCCE by integrating the newly proposed fuzzy extension model into the ensemble framework. RDCFCE adopts the normalized cut algorithm as the consensus function to summarize the fuzzy matrices generated by the fuzzy extension models, partition the consensus matrix, and obtain the final result. Finally, adaptive RDCFCE (A-RDCFCE) is proposed to optimize RDCFCE and improve the performance of RDCFCE further by adopting a self-evolutionary process (SEPP) for the parameter set. Experiments on real cancer gene expression profiles indicate that RDCFCE and A-RDCFCE works well on these data sets, and outperform most of the state-of-the-art tumor clustering algorithms.

Description: Named-entity recognition (NER) plays an important role in the development of biomedical databases. However, the existing NER tools produce multifarious named-entities which may result in both curatable and non-curatable markers. To facilitate biocuration with a straightforward approach, classifying curatable named-entities is helpful with regard to accelerating the biocuration workflow. Co-occurrence Interaction Nexus with Named-entity Recognition (CoINNER) is a web-based tool that allows users to identify genes, chemicals, diseases, and action term mentions in the Comparative Toxicogenomic Database (CTD). To further discover interactions, CoINNER uses multiple advanced algorithms to recognize the mentions in the BioCreative IV CTD Track. CoINNER is developed based on a prototype system that annotated gene, chemical, and disease mentions in PubMed abstracts at BioCreative 2012 Track I (literature triage). We extended our previous system in developing CoINNER. The pre-tagging results of CoINNER were developed based on the state-of-the-art named entity recognition tools in BioCreative III. Next, a method based on conditional random fields (CRFs) is proposed to predict chemical and disease mentions in the articles. Finally, action term mentions were collected by latent Dirichlet allocation (LDA). At the BioCreative IV CTD Track, the best F-measures reached for gene/protein, chemical/drug and disease NER were 54 percent while CoINNER achieved a 61.5 percent F-measure. System URL: http://ikmbio.csie.ncku.edu.tw/coinner/introduction.htm.

Description: Next-generation short-read sequencing is widely utilized in genomic studies. Biological applications require an alignment step to map sequencing reads to the reference genome, before acquiring expected genomic information. This requirement makes alignment accuracy a key factor for effective biological interpretation. Normally, when accounting for measurement errors and single nucleotide polymorphisms, short read mappings with a few mismatches are generally considered acceptable. However, to further improve the efficiency of short-read sequencing alignment, we propose a method to retrieve additional reliably aligned reads (reads with more than a pre-defined number of mismatches), using a Bayesian-based approach. In this method, we first retrieve the sequence context around the mismatched nucleotides within the already aligned reads; these loci contain the genomic features where sequencing errors occur. Then, using the derived pattern, we evaluate the remaining (typically discarded) reads with more than the allowed number of mismatches, and calculate a score that represents the probability that a specific alignment is correct. This strategy allows the extraction of more reliably aligned reads, therefore improving alignment sensitivity. Implementation: The source code of our tool, ResSeq, can be downloaded from: https://github.com/hrbeubiocenter/Resseq.

Description: In genome assembly graphs, motifs such as tips, bubbles, and cross links are studied in order to find sequencing errors and to understand the nature of the genome. Superbubble, a complex generalization of bubbles, was recently proposed as an important subgraph class for analyzing assembly graphs. At present, a quadratic time algorithm is known. This paper gives an -time algorithm to solve this problem for a graph with $m$ edges.

Description: The papers in this special section focus on software and databases that are central in bioinformatics and computational biology.. These programs are playing more and more important roles in biology and medical research. These papers cover a broad range of topics, including computational genomics and transcriptomics, analysis of biological networks and interactions, drug design, biomedical signal/image analysis, biomedical text mining and ontologies, biological data mining, visualization and integration, and high performance computing application in bioinformatics.

Description: In the computational biology community, machine learning algorithms are key instruments for many applications, including the prediction of gene-functions based upon the available biomolecular annotations. Additionally, they may also be employed to compute similarity between genes or proteins. Here, we describe and discuss a software suite we developed to implement and make publicly available some of such prediction methods and a computational technique based upon Latent Semantic Indexing (LSI), which leverages both inferred and available annotations to search for semantically similar genes. The suite consists of three components. BioAnnotationPredictor is a computational software module to predict new gene-functions based upon Singular Value Decomposition of available annotations. SimilBio is a Web module that leverages annotations available or predicted by BioAnnotationPredictor to discover similarities between genes via LSI. The suite includes also SemSim , a new Web service built upon these modules to allow accessing them programmatically. We integrated SemSim in the Bio Search Computing framework (http://www.bioinformatics.deib.polimi.it/bio-seco/seco/), where users can exploit the Search Computing technology to run multi-topic complex queries on multiple integrated Web services. Accordingly, researchers may obtain ranked answers involving the computation of the functional similarity between genes in support of biomedical knowledge discovery.

Description: Identification of cancer subtypes plays an important role in revealing useful insights into disease pathogenesis and advancing personalized therapy. The recent development of high-throughput sequencing technologies has enabled the rapid collection of multi-platform genomic data (e.g., gene expression, miRNA expression, and DNA methylation) for the same set of tumor samples. Although numerous integrative clustering approaches have been developed to analyze cancer data, few of them are particularly designed to exploit both deep intrinsic statistical properties of each input modality and complex cross-modality correlations among multi-platform input data. In this paper, we propose a new machine learning model, called multimodal deep belief network (DBN), to cluster cancer patients from multi-platform observation data. In our integrative clustering framework, relationships among inherent features of each single modality are first encoded into multiple layers of hidden variables, and then a joint latent model is employed to fuse common features derived from multiple input modalities. A practical learning algorithm, called contrastive divergence (CD), is applied to infer the parameters of our multimodal DBN model in an unsupervised manner. Tests on two available cancer datasets show that our integrative data analysis approach can effectively extract a unified representation of latent features to capture both intra- and cross-modality correlations, and identify meaningful disease subtypes from multi-platform cancer data. In addition, our approach can identify key genes and miRNAs that may play distinct roles in the pathogenesis of different cancer subtypes. Among those key miRNAs, we found that the expression level of miR-29a is highly correlated with survival time in ovarian cancer patients. These results indicate that our multimodal DBN based data analysis approach may have practical applications in cancer pathogenesis studies and provide useful guidelines for personali- ed cancer therapy.

Description: The new dual-pivot Quicksort by Vladimir Yaroslavskiy—used in Oracle’s Java runtime library since version 7—features intriguing asymmetries. They make a basic variant of this algorithm use less comparisons than classic single-pivot Quicksort. In this paper, we extend the analysis to the case where the two pivots are chosen as fixed order statistics of a random sample. Surprisingly, dual-pivot Quicksort then needs more comparisons than a corresponding version of classic Quicksort, so it is clear that counting comparisons is not sufficient to explain the running time advantages observed for Yaroslavskiy’s algorithm in practice. Consequently, we take a more holistic approach and give also the precise leading term of the average number of swaps, the number of executed Java Bytecode instructions and the number of scanned elements, a new simple cost measure that approximates I/O costs in the memory hierarchy. We determine optimal order statistics for each of the cost measures. It turns out that the asymmetries in Yaroslavskiy’s algorithm render pivots with a systematic skew more efficient than the symmetric choice. Moreover, we finally have a convincing explanation for the success of Yaroslavskiy’s algorithm in practice: compared with corresponding versions of classic single-pivot Quicksort, dual-pivot Quicksort needs significantly less I/Os, both with and without pivot sampling.

Description: In this paper, we consider the Unsplittable (hard) Capacitated Facility Location Problem (UCFLP) with uniform capacities and present new approximation algorithms for it. This problem is a generalization of the classical facility location problem where each facility can serve at most u units of demand and each client must be served by exactly one facility. This problem is motivated by its applications in many practical problems including supply chain problems of indivisible goods (Verter in Foundations of location analysis, chapter 2. International series in operations research and management science. Springer, Berlin, 2011 ) and the assignment problem in the content distribution networks (Bateni and Hajiaghayi in Proceedings of the nineteenth annual ACM-SIAM symposium on discrete algorithms, pp 805–814, 2009 ). While there are several approximation algorithms for the soft capacitated version of this problem (in which one can open multiple copies of each facility) or the splittable version (in which the demand of each client can be divided to be served by multiple open facilities), there are very few results for the UCFLP. It is known that it is NP-hard to approximate this problem within any factor without violating the capacities. So we consider bicriteria \((\alpha ,\beta )\) -approximations where the algorithm returns a solution whose cost is within factor \(\alpha \) of the optimum and violates the capacity constraints within factor \(\beta \) . Shmoys et al. (Proceedings of the twenty-ninth annual ACM symposium on theory of computing, pp 265–274, 1997 ) were the first to consider this problem and gave a (9, 4)-approximation. Later results imply ( O (1), 2)-approximations, however, no constant factor approximation is known with capacity violation of less than 2. We present a framework for designing bicriteria approximation algorithms for this problem and show two new approximation algorithms with factors (9, 3 / 2) and (29.315, 4 / 3). These are the first algorithms with constant approximation in which the violation of capacities is below 2. The heart of our algorithm is a reduction from the UCFLP to a restricted version of the problem. One feature of this reduction is that any \((O(1),1+{\epsilon })\) -approximation for the restricted version implies an \((O(1),1+{\epsilon })\) -approximation for the UCFLP and we believe our techniques might be useful towards finding such approximations or perhaps \((f({\epsilon }),1+{\epsilon })\) -approximation for the UCFLP for some function f . In addition, we present a quasi-polynomial time \((1+\epsilon ,1+\epsilon )\) -approximation for the (uniform) UCFLP in Euclidean metrics, for any constant \({\epsilon }〉0\) .

Description: The papers in this special issue contain extended versions of works that were originally presented at the Brazilian Symposium on Bioinformatics 2013 (BSB 2013), held in Recife, Brazil, November 3-6, 2013.

Description: Computational methods for predicting protein-protein interactions are important tools that can complement high-throughput technologies and guide biologists in designing new laboratory experiments. The proteins and the interactions between them can be described by a network which is characterized by several topological properties. Information about proteins and interactions between them, in combination with knowledge about topological properties of the network, can be used for developing computational methods that can accurately predict unknown protein-protein interactions. This paper presents a supervised learning framework based on Bayesian inference for combining two types of information: i) network topology information, and ii) information related to proteins and the interactions between them. The motivation of our model is that by combining these two types of information one can achieve a better accuracy in predicting protein-protein interactions, than by using models constructed from these two types of information independently.

Description: We develop a theory of algebraic operations over linear and context-free grammars that makes it possible to combine simple “atomic” grammars operating on single sequences into complex, multi-dimensional grammars. We demonstrate the utility of this framework by constructing the search spaces of complex alignment problems on multiple input sequences explicitly as algebraic expressions of very simple one-dimensional grammars. In particular, we provide a fully worked frameshift-aware, semiglobal DNA-protein alignment algorithm whose grammar is composed of products of small, atomic grammars. The compiler accompanying our theory makes it easy to experiment with the combination of multiple grammars and different operations. Composite grammars can be written out in $ {rm L}^AT_{E}X$ for documentation and as a guide to implementation of dynamic programming algorithms. An embedding in Haskell as a domain-specific language makes the theory directly accessible to writing and using grammar products without the detour of an external compiler. Software and supplemental files available here: http://www.bioinf.uni-leipzig.de/Software/gramprod/

Description: Recent advancements in genomics and proteomics provide a solid foundation for understanding the pathogenesis of diabetes. Proteomics of diabetes associated pathways help to identify the most potent target for the management of diabetes. The relevant datasets are scattered in various prominent sources which takes much time to select the therapeutic target for the clinical management of diabetes. However, additional information about target proteins is needed for validation. This lacuna may be resolved by linking diabetes associated genes, pathways and proteins and it will provide a strong base for the treatment and planning management strategies of diabetes. Thus, a web source “Diabetes Associated Proteins Database (DAPD)” has been developed to link the diabetes associated genes, pathways and proteins using PHP, MySQL. The current version of DAPD has been built with proteins associated with different types of diabetes. In addition, DAPD has been linked to external sources to gain the access to more participatory proteins and their pathway network. DAPD will reduce the time and it is expected to pave the way for the discovery of novel anti-diabetic leads using computational drug designing for diabetes management. DAPD is open accessed via following url www.mkarthikeyan.bioinfoau.org/dapd.

Description: Determining the glycan topology automatically from mass spectra represents a great challenge. Existing methods fall into approximate and exact ones. The former including greedy and heuristic ones can reduce the computational complexity, but suffer from information lost in the procedure of glycan interpretation. The latter including dynamic programming and exhaustive enumeration are much slower than the former. In the past years, nearly all emerging methods adopted a tree structure to represent a glycan. They share such problems as repetitive peak counting in reconstructing a candidate structure. Besides, tree-based glycan representation methods often have to give different computational formulas for binary and ternary glycans. We propose a new directed acyclic graph structure for glycan representation. Based on it, this work develops a de novo algorithm to accurately reconstruct the tree structure iteratively from mass spectra with logical constraints and some known biosynthesis rules, by a single computational formula. The experiments on multiple complex glycans extracted from human serum show that the proposed algorithm can achieve higher accuracy to determine a glycan topology than prior methods without increasing computational burden.

Description: A crucial step in understanding the architecture of cells and tissues from microscopy images, and consequently explain important biological events such as wound healing and cancer metastases, is the complete extraction and enumeration of individual filaments from the cellular cytoskeletal network. Current efforts at quantitative estimation of filament length distribution, architecture and orientation from microscopy images are predominantly limited to visual estimation and indirect experimental inference. Here we demonstrate the application of a new algorithm to reliably estimate centerlines of biological filament bundles and extract individual filaments from the centerlines by systematically disambiguating filament intersections. We utilize a filament enhancement step followed by reverse diffusion based filament localization and an integer programming based set combination to systematically extract accurate filaments automatically from microscopy images. Experiments on simulated and real confocal microscope images of flat cells (2D images) show efficacy of the new method.

Description: The Local/Global Alignment (Zemla, 2003), or LGA, is a popular method for the comparison of protein structures. One of the two components of LGA requires us to compute the longest common contiguous segments between two protein structures. That is, given two structures $A=(a_1, ldots , a_n)$ and $B=(b_1, ldots , b_n)$ where $a_k$ , $b_kin mathbb {R}^3$ , we are to find, among all the segments $f=(a_i,ldots ,a_j)$ and $g=(b_i,ldots ,b_j)$ that fulfill a certain criterion regarding their similarity, those of the maximum length. We consider the following criteria: (1) the root mean squared deviation (RMSD) between $f$ and $g$ is to be within a given $tin mathbb {R}$ ; (2) $f$ and $g$ can be superposed such that for each $k$ , $ile kle j$ , $Vert a_k-b_kVert le t$ for a given $tin mathbb {R}$ . We give an algorithm of $O(n;log; n+n{{boldsymbol l}})$ time complexity when the first requirement applies, where ${{boldsymbol l}}$ is the maximum length of the segments fulfilling the criterion. We show an FPTAS which, for any

Description: Noise can induce various dynamical behaviors in nonlinear systems. White noise perturbed systems have been extensively investigated during the last decades. In gene networks, experimentally observed extrinsic noise is colored. As an attempt, we investigate the genetic toggle switch systems perturbed by colored extrinsic noise and with kinetic parameters. Compared with white noise perturbed systems, we show there also exists optimal colored noise strength to induce the best stochastic switch behaviors in the single toggle switch, and the best synchronized switching in the networked systems, which demonstrate that noise-induced optimal switch behaviors are widely in existence. Moreover, under a wide range of system parameter regions, we find there exist wider ranges of white and colored noises strengths to induce good switch and synchronization behaviors, respectively; therefore, white noise is beneficial for switch and colored noise is beneficial for population synchronization. Our observations are very robust to extrinsic stimulus strength, cell density, and diffusion rate. Finally, based on the Waddington’s epigenetic landscape and the Wiener-Khintchine theorem, physical mechanisms underlying the observations are interpreted. Our investigations can provide guidelines for experimental design, and have potential clinical implications in gene therapy and synthetic biology.

Description: Revealing the underlying evolutionary mechanism plays an important role in understanding protein interaction networks in the cell. While many evolutionary models have been proposed, the problem about applying these models to real network data, especially for differentiating which model can better describe evolutionary process for the observed network remains a challenge. The traditional way is to use a model with presumed parameters to generate a network, and then evaluate the fitness by summary statistics, which however cannot capture the complete network structures information and estimate parameter distribution. In this work, we developed a novel method based on Approximate Bayesian Computation and modified Differential Evolution algorithm (ABC-DEP) that is capable of conducting model selection and parameter estimation simultaneously and detecting the underlying evolutionary mechanisms for PPI networks more accurately. We tested our method for its power in differentiating models and estimating parameters on simulated data and found significant improvement in performance benchmark, as compared with a previous method. We further applied our method to real data of protein interaction networks in human and yeast. Our results show duplication attachment model as the predominant evolutionary mechanism for human PPI networks and Scale-Free model as the predominant mechanism for yeast PPI networks.

Description: Single nucleotide polymorphisms, a dominant type of genetic variants, have been used successfully to identify defective genes causing human single gene diseases. However, most common human diseases are complex diseases and caused by gene-gene and gene-environment interactions. Many SNP-SNP interaction analysis methods have been introduced but they are not powerful enough to discover interactions more than three SNPs. The paper proposes a novel method that analyzes all SNPs simultaneously. Different from existing methods, the method regards an individual’s genotype data on a list of SNPs as a point with a unit of energy in a multi-dimensional space, and tries to find a new coordinate system where the energy distribution difference between cases and controls reaches the maximum. The method will find different multiple SNPs combinatorial patterns between cases and controls based on the new coordinate system. The experiment on simulated data shows that the method is efficient. The tests on the real data of age-related macular degeneration (AMD) disease show that it can find out more significant multi-SNP combinatorial patterns than existing methods.

Description: Disulfide connectivity is an important protein structural characteristic. Accurately predicting disulfide connectivity solely from protein sequence helps to improve the intrinsic understanding of protein structure and function, especially in the post-genome era where large volume of sequenced proteins without being functional annotated is quickly accumulated. In this study, a new feature extracted from the predicted protein 3D structural information is proposed and integrated with traditional features to form discriminative features. Based on the extracted features, a random forest regression model is performed to predict protein disulfide connectivity. We compare the proposed method with popular existing predictors by performing both cross-validation and independent validation tests on benchmark datasets. The experimental results demonstrate the superiority of the proposed method over existing predictors. We believe the superiority of the proposed method benefits from both the good discriminative capability of the newly developed features and the powerful modelling capability of the random forest. The web server implementation, called TargetDisulfide, and the benchmark datasets are freely available at: http://csbio.njust.edu.cn/bioinf/TargetDisulfide for academic use.

Description: Proteins are molecules that form the mass of living beings. These proteins exist in dissociated forms like amino-acids and carry out various biological functions, in fact, almost all body reactions occur with the participation of proteins. This is one of the reasons why the analysis of proteins has become a major issue in biology. In a more concrete way, the identification of conserved patterns in a set of related protein sequences can provide relevant biological information about these protein functions. In this paper, we present a novel algorithm based on teaching learning based optimization (TLBO) combined with a local search function specialized to predict common patterns in sets of protein sequences. This population-based evolutionary algorithm defines a group of individuals (solutions) that enhance their knowledge (quality) by means of different learning stages. Thus, if we correctly adapt it to the biological context of the mentioned problem, we can get an acceptable set of quality solutions. To evaluate the performance of the proposed technique, we have used six instances composed of different related protein sequences obtained from the PROSITE database. As we will see, the designed approach makes good predictions and improves the quality of the solutions found by other well-known biological tools.

Description: We introduce Supervised Variational Relevance Learning (Suvrel), a variational method to determine metric tensors to define distance based similarity in pattern classification, inspired in relevance learning. The variational method is applied to a cost function that penalizes large intraclass distances and favors small interclass distances. We find analytically the metric tensor that minimizes the cost function. Preprocessing the patterns by doing linear transformations using the metric tensor yields a dataset which can be more efficiently classified. We test our methods using publicly available datasets, for some standard classifiers. Among these datasets, two were tested by the MAQC-II project and, even without the use of further preprocessing, our results improve on their performance.

Description: Bandwidth reservation has been recognized as a value-added service to the cloud provider in recent years. We consider an open market of cloud bandwidth reservation, in which cloud providers offer bandwidth reservation services to cloud tenants, especially online streaming service providers, who have strict requirements on the amount of bandwidth to guarantee their quality of services. In this paper, we model the open market as a double-sided auction, and propose the first family of ST rategy-proof double A uctions for multi-cloud, multi-tenant bandwidth R eservation (STAR). STAR contains two auction mechanisms. The first one, STAR-Grouping, divides the tenants into groups by a bid-independent way, and carefully matches the cloud providers with the tenant groups to form good trades. The second one, STAR-Padding, greedily matches the cloud providers with the tenants, and fills the partially reserved cloud provider(s) with a novel virtual padding tenant who can be a component of the auctioneer. Our analysis shows that both of the two auction mechanisms achieve strategy-proofness and ex-post budget balance. Our evaluation results show that they achieve good performance in terms of social welfare, cloud bandwidth utilization, and tenant satisfaction ratio.

Description: In a distributed real-time system (DRTS), jobs are often executed on a number of processors and must complete by their end-to-end deadlines. Job deadline requirements may be violated if resource competition among different jobs on a given processor is not considered. This paper introduces a distributed, locally optimal algorithm to assign local deadlines to the jobs on each processor without any restrictions on the mappings of the applications to the processors in the distributed soft real-time system. Improvedschedulability results are achieved by the algorithm since disparate workloads among the processors due to competing jobs havingdifferent paths are considered. Given its distributed nature, the proposed algorithm is adaptive to dynamic changes of the applications and avoids the overhead of global clock synchronization. In order to make the proposed algorithm more practical, two derivatives of the algorithm are proposed and compared. Simulation results based on randomly generated workloads indicate that the proposed approach outperforms existing work both in terms of the number of feasible jobs (between 51% and 313% on average) and the number of feasible task sets (between 12% and 71% on average).

Description: Reproducibility, i.e. getting bitwise identical floating point results from multiple runs of the same program, is a property that many users depend on either for debugging or correctness checking in many codes [10] . However, the combination of dynamic scheduling of parallel computing resources, and floating point nonassociativity, makes attaining reproducibility a challenge even for simple reduction operations like computing the sum of a vector of numbers in parallel. We propose a technique for floating point summation that is reproducible independent of the order of summation. Our technique uses Rump’s algorithm for error-free vector transformation [7] , and is much more efficient than using (possibly very) high precision arithmetic. Our algorithm reproducibly computes highly accurate results with an absolute error bound of $n cdot 2^{-28} cdot macheps cdot max _i |v_i|$ at a cost of $7n$ FLOPs and a small constant amount of extra memory usage. Higher accuracies are also possible by increasing the number of error-free transformations. As long as all operations are performed in to-nearest rounding mode, results computed by the proposed algorithms are reproducible for any run on any platform. In particular, our algorithm requires the minimum number of reductions, i.e. one reduction of an array of six double precision floating point numbers per sum, and hence is well suited for massively parallel environments.

Description: In recent years, embedded dynamic random-access memory (eDRAM) technology has been implemented in last-level caches due to its low leakage energy consumption and high density. However, the fact that eDRAM presents slower access time than static RAM (SRAM) technology has prevented its inclusion in higher levels of the cache hierarchy. This paper proposes to mingle SRAM and eDRAM banks within the data array of second-level (L2) caches. The main goal is to achieve the best trade-off among performance, energy, and area. To this end, two main directions have been followed. First, this paper explores the optimal percentage of banks for each technology. Second, the cache controller is redesigned to deal with performance and energy. Performance is addressed by keeping the most likely accessed blocks in fast SRAM banks. In addition, energy savings are further enhanced by avoiding unnecessary destructive reads of eDRAM blocks. Experimental results show that, compared to a conventional SRAM L2 cache, a hybrid approach requiring similar or even lower area speedups the performance on average by 5.9 percent, while the total energy savings are by 32 percent. For a 45 nm technology node, the energy-delay-area product confirms that a hybrid cache is a better design than the conventional SRAM cache regardless of the number of eDRAM banks, and also better than a conventional eDRAM cache when the number of SRAM banks is an eighth of the total number of cache banks.

Description: Nearly all of the currently used signature schemes, such as RSA or DSA, are based either on the factoring assumption or the presumed intractability of the discrete logarithm problem. As a consequence, the appearance of quantum computers or algorithmic advances on these problems may lead to the unpleasant situation that a large number of today’s schemes will most likely need to be replaced with more secure alternatives. In this work we present such an alternative—an efficient signature scheme whose security is derived from the hardness of lattice problems. It is based on recent theoretical advances in lattice-based cryptography and is highly optimized for practicability and use in embedded systems. The public and secret keys are roughly $1.5$  kB and $0.3$  kB long, while the signature size is approximately $1.1$  kB for a security level of around $80$ bits. We provide implementation results on reconfigurable hardware (Spartan/Virtex-6) and demonstrate that the scheme is scalable, has low area consumption, and even outperforms classical schemes.

Description: With the rising demands on cloud services, the electricity consumption has been increasing drastically as the main operational expenditure (OPEX) to data center providers. The geographical heterogeneity of electricity prices motivates us to study the task placement problem over geo-distributed data centers. We exploit the dynamic frequency scaling technique and formulate an optimization problem that minimizes OPEX while guaranteeing the quality-of-service, i.e., the expected response time of tasks. Furthermore, an optimal solution is discovered for this formulated problem. The experimental results show that our proposal achieves much higher cost-efficiency than the traditional resizing scheme, i.e., by activating/deactivating certain servers in data centers.

Description: A new methodology for DRAM performance analysis has been proposed based on accurate characterization of DRAM bus cycles. The proposed methodology allows cycle-accurate performance analysis of arbitrary DRAM traces, obviates the need for functional simulations, allows accurate estimation of DRAM performance maximum, and enables root causing of suboptimal DRAM operation.

Description: Genes can participate in multiple biological processes at a time and thus their expression can be seen as a composition of the contributions from the active processes. Biclustering under a plaid assumption allows the modeling of interactions between transcriptional modules or biclusters (subsets of genes with coherence across subsets of conditions) by assuming an additive composition of contributions in their overlapping areas. Despite the biological interest of plaid models, few biclustering algorithms consider plaid effects and, when they do, they place restrictions on the allowed types and structures of biclusters, and suffer from robustness problems by seizing exact additive matchings. We propose BiP (Biclustering using Plaid models), a biclustering algorithm with relaxations to allow expression levels to change in overlapping areas according to biologically meaningful assumptions (weighted and noise-tolerant composition of contributions). BiP can be used over existing biclustering solutions (seizing their benefits) as it is able to recover excluded areas due to unaccounted plaid effects and detect noisy areas non-explained by a plaid assumption, thus producing an explanatory model of overlapping transcriptional activity. Experiments on synthetic data support BiP’s efficiency and effectiveness. The learned models from expression data unravel meaningful and non-trivial functional interactions between biological processes associated with putative regulatory modules.

Description: We propose a classifier system called iPFPi that predicts the functions of un-annotated proteins. iPFPi assigns an un-annotated protein $P$ the functions of GO annotation terms that are semantically similar to $P$ . An un-annotated protein $P$ and a GO annotation term $T$ are represented by their characteristics. The characteristics of $P$ are GO terms found within the abstracts of biomedical literature associated with $P$ . The characteristics of $T$ are GO terms found within the abstracts of biomedical literature associated with the proteins annotated with the function of $T$ . Let - F$ and $Fprime $ be the important (dominant) sets of characteristic terms representing $T$ and $P$ , respectively. iPFPi would annotate $P$ with the function of $T$ , if $F$ and $Fprime $ are semantically similar. We constructed a novel semantic similarity measure that takes into consideration several factors, such as the dominance degree of each characteristic term $t$ in set $F$

Description: Adverse drug reaction (ADR) is a common clinical problem, sometimes accompanying with high risk of mortality and morbidity. It is also one of the major factors that lead to failure in new drug development. Unfortunately, most of current experimental and computational methods are unable to evaluate clinical safety of drug candidates in early drug discovery stage due to the very limited knowledge of molecular mechanisms underlying ADRs. Therefore, in this study, we proposed a novel naïve Bayesian model for rapid assessment of clinical ADRs with frequency estimation. This model was constructed on a gene-ADR association network, which covered 611 US FDA approved drugs, 14,251 genes, and 1,254 distinct ADR terms. An average detection rate of 99.86 and 99.73 percent were achieved eventually in identification of known ADRs in internal test data set and external case analyses respectively. Moreover, a comparative analysis between the estimated frequencies of ADRs and their observed frequencies was undertaken. It is observed that these two frequencies have the similar distribution trend. These results suggest that the naïve Bayesian model based on gene-ADR association network can serve as an efficient and economic tool in rapid ADRs assessment.

Description: The papers in this special section were presented at the 13th International Workshop on Data Mining in Bioinformatics (BIOKDD???14) was organized in conjunction with the ACM SIGKDD International Conference on Knowledge Discovery and Data Mining that was held on August 24, 2014 in New York, NY. It brought together international researchers in the interacting disciplines of data mining, systems biology, and bioinformatics at the Bloomberg Headquarters venue. The goal of this workshop is to encourage Knowledge Discovery and Data mining (KDD) researchers to take on the numerous challenges that Bioinformatics offers.

Description: The introduction of next-generation sequencing technologies has radically changed the way we view structural genetic events. Microhomology-mediated break-induced replication (MMBIR) is just one of the many mechanisms that can cause genomic destabilization that may lead to cancer. Although the mechanism for MMBIR remains unclear, it has been shown that MMBIR is typically associated with template-switching events. Currently, to our knowledge, there is no existing bioinformatics tool to detect these template-switching events. We have developed MMBIRFinder, a method that detects template-switching events associated with MMBIR from whole-genome sequenced data. MMBIRFinder uses a half-read alignment approach to identify potential regions of interest. Clustering of these potential regions helps narrow the search space to regions with strong evidence. Subsequent local alignments identify the template-switching events with single-nucleotide accuracy. Using simulated data, MMBIRFinder identified 83 percent of the MMBIR regions within a five nucleotide tolerance. Using real data, MMBIRFinder identified 16 MMBIR regions on a normal breast tissue data sample and 51 MMBIR regions on a triple-negative breast cancer tumor sample resulting in detection of 37 novel template-switching events. Finally, we identified template-switching events residing in the promoter region of seven genes that have been implicated in breast cancer. The program is freely available for download at https://github.com/msegar/MMBIRFinder.

Description: Compressing heterogeneous collections of trees is an open problem in computational phylogenetics. In a heterogeneous tree collection, each tree can contain a unique set of taxa. An ideal compression method would allow for the efficient archival of large tree collections and enable scientists to identify common evolutionary relationships over disparate analyses. In this paper, we extend TreeZip to compress heterogeneous collections of trees. TreeZip is the most efficient algorithm for compressing homogeneous tree collections. To the best of our knowledge, no other domain-based compression algorithm exists for large heterogeneous tree collections or enable their rapid analysis. Our experimental results indicate that TreeZip averages 89.03 percent (72.69 percent) space savings on unweighted (weighted) collections of trees when the level of heterogeneity in a collection is moderate. The organization of the TRZ file allows for efficient computations over heterogeneous data. For example, consensus trees can be computed in mere seconds. Lastly, combining the TreeZip compressed (TRZ) file with general-purpose compression yields average space savings of 97.34 percent (81.43 percent) on unweighted (weighted) collections of trees. Our results lead us to believe that TreeZip will prove invaluable in the efficient archival of tree collections, and enables scientists to develop novel methods for relating heterogeneous collections of trees.

Description: The papers in this special section were presented at the 2014 International Conference on Genome Informatics (GIW).

Description: Cluster analysis of biological networks is one of the most important approaches for identifying functional modules and predicting protein functions. Furthermore, visualization of clustering results is crucial to uncover the structure of biological networks. In this paper, ClusterViz, an APP of Cytoscape 3 for cluster analysis and visualization, has been developed. In order to reduce complexity and enable extendibility for ClusterViz, we designed the architecture of ClusterViz based on the framework of Open Services Gateway Initiative. According to the architecture, the implementation of ClusterViz is partitioned into three modules including interface of ClusterViz, clustering algorithms and visualization and export. ClusterViz fascinates the comparison of the results of different algorithms to do further related analysis. Three commonly used clustering algorithms, FAG-EC, EAGLE and MCODE, are included in the current version. Due to adopting the abstract interface of algorithms in module of the clustering algorithms, more clustering algorithms can be included for the future use. To illustrate usability of ClusterViz, we provided three examples with detailed steps from the important scientific articles, which show that our tool has helped several research teams do their research work on the mechanism of the biological networks.

Description: Structural domains are evolutionary and functional units of proteins and play a critical role in comparative and functional genomics. Computational assignment of domain function with high reliability is essential for understanding whole-protein functions. However, functional annotations are conventionally assigned onto full-length proteins rather than associating specific functions to the individual structural domains. In this article, we present Structural Domain Annotation (SDA), a novel computational approach to predict functions for SCOP structural domains. The SDA method integrates heterogeneous information sources, including structure alignment based protein-SCOP mapping features, InterPro2GO mapping information, PSSM Profiles, and sequence neighborhood features, with a Bayesian network. By large-scale annotating Gene Ontology terms to SCOP domains with SDA, we obtained a database of SCOP domain to Gene Ontology mappings, which contains $sim$ 162,000 out of the approximately 166,900 domains in SCOPe 2.03 ( $>$ 97 percent) and their predicted Gene Ontology functions. We have benchmarked SDA using a single-domain protein dataset and an independent dataset from different species. Comparative studies show that SDA significantly outperforms the existing function prediction methods for structural domains in terms of coverage and maximum F-measure.

Description: A major challenge in computational biology is to find simple representations of high-dimensional data that best reveal the underlying structure. In this work, we present an intuitive and easy-to-implement method based on ranked neighborhood comparisons that detects structure in unsupervised data. The method is based on ordering objects in terms of similarity and on the mutual overlap of nearest neighbors. This basic framework was originally introduced in the field of social network analysis to detect actor communities. We demonstrate that the same ideas can successfully be applied to biomedical data sets in order to reveal complex underlying structure. The algorithm is very efficient and works on distance data directly without requiring a vectorial embedding of data. Comprehensive experiments demonstrate the validity of this approach. Comparisons with state-of-the-art clustering methods show that the presented method outperforms hierarchical methods as well as density based clustering methods and model-based clustering. A further advantage of the method is that it simultaneously provides a visualization of the data. Especially in biomedical applications, the visualization of data can be used as a first pre-processing step when analyzing real world data sets to get an intuition of the underlying data structure. We apply this model to synthetic data as well as to various biomedical data sets which demonstrate the high quality and usefulness of the inferred structure.

Description: Proline residues are common source of kinetic complications during folding. The X-Pro peptide bond is the only peptide bond for which the stability of the cis and trans conformations is comparable. The cis-trans isomerization (CTI) of X-Pro peptide bonds is a widely recognized rate-limiting factor, which can not only induces additional slow phases in protein folding but also modifies the millisecond and sub-millisecond dynamics of the protein. An accurate computational prediction of proline CTI is of great importance for the understanding of protein folding, splicing, cell signaling, and transmembrane active transport in both the human body and animals. In our earlier work, we successfully developed a biophysically motivated proline CTI predictor utilizing a novel tree-based consensus model with a powerful metalearning technique and achieved 86.58 percent Q2 accuracy and 0.74 Mcc, which is a better result than the results (70-73 percent Q2 accuracies) reported in the literature on the well-referenced benchmark dataset. In this paper, we describe experiments with novel randomized subspace learning and bootstrap seeding techniques as an extension to our earlier work, the consensus models as well as entropy-based learning methods, to obtain better accuracy through a precise and robust learning scheme for proline CTI prediction.

Description: Efficient search algorithms for finding genomic-range overlaps are essential for various bioinformatics applications. A majority of fast algorithms for searching the overlaps between a query range (e.g., a genomic variant) and a set of N reference ranges (e.g., exons) has time complexity of O ( k + log N ), where k denotes a term related to the length and location of the reference ranges. Here, we present a simple but efficient algorithm that reduces k, based on the maximum reference range length. Specifically, for a given query range and the maximum reference range length, the proposed method divides the reference range set into three subsets: always , potentially , and never overlapping . Therefore, search effort can be reduced by excluding never overlapping subset. We demonstrate that the running time of the proposed algorithm is proportional to potentially overlapping subset size, that is proportional to the maximum reference range length if all the other conditions are the same. Moreover, an implementation of our algorithm was 13.8 to 30.0 percent faster than one of the fastest range search methods available when tested on various genomic-range data sets. The proposed algorithm has been incorporated into a disease-linked variant prioritization pipeline for WGS (http://gnome.tchlab.org) and its implementation is available at http://ml.ssu.ac.kr/gSearch.

Description: The identification of protein complexes in protein-protein interaction (PPI) networks is fundamental for understanding biological processes and cellular molecular mechanisms. Many graph computational algorithms have been proposed to identify protein complexes from PPI networks by detecting densely connected groups of proteins. These algorithms assess the density of subgraphs through evaluation of the sum of individual edges or nodes; thus, incomplete and inaccurate measures may miss meaningful biological protein complexes with functional significance. In this study, we propose a novel method for assessing the compactness of local subnetworks by measuring the number of three node cliques. The present method detects each optimal cluster by growing a seed and maximizing the compactness function. To demonstrate the efficacy of the new proposed method, we evaluate its performance using five PPI networks on three reference sets of yeast protein complexes with five different measurements and compare the performance of the proposed method with four state-of-the-art methods. The results show that the protein complexes generated by the proposed method are of better quality than those generated by four classic methods. Therefore, the new proposed method is effective and useful for detecting protein complexes in PPI networks.

Description: A commonly studied means of parameterizing graph problems is the deletion distance from triviality (Guo et al., Parameterized and exact computation, Springer, Berlin, pp. 162–173, 2004 ), which counts vertices that need to be deleted from a graph to place it in some class for which efficient algorithms are known. In the context of graph isomorphism, we define triviality to mean a graph with maximum degree bounded by a constant, as such graph classes admit polynomial-time isomorphism tests. We generalise deletion distance to a measure we call elimination distance to triviality, based on elimination trees or tree-depth decompositions. We establish that graph canonisation, and thus graph isomorphism, is \(\mathsf {FPT}\) when parameterized by elimination distance to bounded degree, extending results of Bouland et al. (Parameterized and exact computation, Springer, Berlin, pp. 218–230, 2012 ).

Description: Recent advances in drift analysis have given us better and better tools for understanding random processes, including the run time of randomized search heuristics. In the setting of multiplicative drift we do not only have excellent bounds on the expected run time, but also more general results showing the strong concentration of the run time. In this paper we investigate the setting of additive drift under the assumption of strong concentration of the “step size” of the process. Under sufficiently strong drift towards the goal we show a strong concentration of the hitting time. In contrast to this, we show that in the presence of small drift a Gambler’s-Ruin-like behavior of the process overrides the influence of the drift, leading to a maximal movement of about \(\sqrt{t}\) steps within t iterations. Finally, in the presence of sufficiently strong negative drift the hitting time is superpolynomial with high probability; this corresponds to the well-known Negative Drift Theorem.

Description: Binets and trinets are phylogenetic networks with two and three leaves, respectively. Here we consider the problem of deciding if there exists a binary level-1 phylogenetic network displaying a given set  \(\mathbb {T}\) of binary binets or trinets over a taxon set  X , and constructing such a network whenever it exists. We show that this is NP-hard for trinets but polynomial-time solvable for binets. Moreover, we show that the problem is still polynomial-time solvable for inputs consisting of binets and trinets as long as the cycles in the trinets have size three. Finally, we present an  \(O(3^{|X|} poly(|X|))\) time algorithm for general sets of binets and trinets. The latter two algorithms generalise to instances containing level-1 networks with arbitrarily many leaves, and thus provide some of the first supernetwork algorithms for computing networks from a set of rooted phylogenetic networks.

Description: We consider stochastic versions of OneMax and LeadingOnes and analyze the performance of evolutionary algorithms with and without populations on these problems. It is known that the ( \(1+1\) ) EA on OneMax performs well in the presence of very small noise, but poorly for higher noise levels. We extend these results to LeadingOnes and to many different noise models, showing how the application of drift theory can significantly simplify and generalize previous analyses. Most surprisingly, even small populations (of size \(\varTheta (\log n)\) ) can make evolutionary algorithms perform well for high noise levels, well outside the abilities of the ( \(1+1\) ) EA. Larger population sizes are even more beneficial; we consider both parent and offspring populations. In this sense, populations are robust in these stochastic settings.

Description: Since Tinhofer proposed the MinGreedy algorithm for maximum cardinality matching in 1984, several experimental studies found the randomized algorithm to perform excellently for various classes of random graphs and benchmark instances. In contrast, only few analytical results are known. We show that MinGreedy cannot improve on the trivial approximation ratio of  \(\frac{1}{2}\) whp., even for bipartite graphs. Our hard inputs seem to require a small number of high-degree nodes. This motivates an investigation of greedy algorithms on graphs with maximum degree  \(\varDelta \) : we show that  MinGreedy achieves a  \({\frac{{\varDelta }-1}{2{\varDelta }-3}} \) -approximation for graphs with  \({\varDelta } {=} 3\) and for \(\varDelta \) -regular graphs, and a guarantee of  \({\frac{{\varDelta }-1/2}{2{\varDelta }-2}} \) for graphs with maximum degree  \({\varDelta } \) . Interestingly, our bounds even hold for the deterministic MinGreedy that breaks all ties arbitrarily. Moreover, we investigate the limitations of the greedy paradigm, using the model of priority algorithms introduced by Borodin, Nielsen, and Rackoff. We study deterministic priority algorithms and prove a  \({\frac{{\varDelta }-1}{2{\varDelta }-3}}\) -inapproximability result for graphs with maximum degree  \({\varDelta } \) ; thus, these greedy algorithms do not achieve a  \(\frac{1}{2} {+} \varepsilon \) -approximation and in particular the  \(\frac{2}{3}\) -approximation obtained by the deterministic MinGreedy for  \({\varDelta } {=} 3\) is optimal in this class. For  k -uniform hypergraphs we show a tight  \(\frac{1}{k}\) -inapproximability bound. We also study fully randomized priority algorithms and give a  \(\frac{5}{6}\) -inapproximability bound. Thus, they cannot compete with matching algorithms of other paradigms.

Description: We discuss how string sorting algorithms can be parallelized on modern multi-core shared memory machines. As a synthesis of the best sequential string sorting algorithms and successful parallel sorting algorithms for atomic objects, we first propose string sample sort. The algorithm makes effective use of the memory hierarchy, uses additional word level parallelism, and largely avoids branch mispredictions. Then we focus on NUMA architectures, and develop parallel multiway LCP-merge and -mergesort to reduce the number of random memory accesses to remote nodes. Additionally, we parallelize variants of multikey quicksort and radix sort that are also useful in certain situations. As base-case sorter for LCP-aware string sorting we describe sequential LCP-insertion sort which calculates the LCP array and accelerates its insertions using it. Comprehensive experiments on five current multi-core platforms are then reported and discussed. The experiments show that our parallel string sorting implementations scale very well on real-world inputs and modern machines.

Description: Stochastic boolean function evaluation (SBFE) is the problem of determining the value of a given boolean function f on an unknown input x , when each bit \(x_i\) of x can only be determined by paying a given associated cost \(c_i\) . Further, x is drawn from a given product distribution: for each \(x_i\) , \(\mathbf{Pr}[x_i=1] = p_i\) and the bits are independent. The goal is to minimize the expected cost of evaluation. In this paper, we study the complexity of the SBFE problem for classes of DNF formulas. We consider both exact and approximate versions of the problem for subclasses of DNF, for arbitrary costs and product distributions, and for unit costs and/or the uniform distribution.

Description: Interval graphs are intersection graphs of closed intervals of the real-line. The well-known computational problem, called recognition , asks whether an input graph G can be represented by closed intervals, i.e., whether G is an interval graph. There are several linear-time algorithms known for recognizing interval graphs, the oldest one is by Booth and Lueker (J Comput Syst Sci 13:335–379, 1976 ) based on PQ-trees. In this paper, we study a generalization of recognition, called partial representation extension . The input of this problem consists of a graph G with a partial representation \({{{\mathcal {R}}}}'\) fixing the positions of some intervals. The problem asks whether it is possible to place the remaining interval and create an interval representation \({{{\mathcal {R}}}}\) of the entire graph G extending \({{{\mathcal {R}}}}'\) . We generalize the characterization of interval graphs by Fulkerson and Gross (Pac J Math 15:835–855, 1965 ) to extendible partial representations. Using it, we give a linear-time algorithm for partial representation extension based on a reordering problem of PQ-trees.

Description: Modern data management systems often need to deal with massive, dynamic and inherently distributed data sources. We collect the data using a distributed network, and at the same time try to maintain a global view of the data at a central coordinator using a minimal amount of communication. Such applications have been captured by the distributed monitoring model which has attracted a lot of attention in recent years. In this paper we investigate the monitoring of the entropy functions, which are very useful in network monitoring applications such as detecting distributed denial-of-service attacks. Our results improve the previous best results by Arackaparambil et al. in ICLP 1: 95–106 ( 2009 ). Our technical contribution also includes implementing the celebrated AMS sampling method (by Alon et al. in J Comput Syst Sci 58(1): 137–147 1999 ) in the distributed monitoring model, which could be of independent interest.

Description: In the Boundary Labeling problem, we are given a set of  n points, referred to as sites , inside an axis-parallel rectangle  R , and a set of  n pairwise disjoint rectangular labels that are attached to  R from the outside. The task is to connect the sites to the labels by non-intersecting rectilinear paths, so-called leaders , with at most one bend. In this paper, we study the Multi-Sided Boundary Labeling problem, with labels lying on at least two sides of the enclosing rectangle. We present a polynomial-time algorithm that computes a crossing-free leader layout if one exists. So far, such an algorithm has only been known for the cases in which labels lie on one side or on two opposite sides of  R (here a crossing-free solution always exists). The case where labels may lie on adjacent sides is more difficult. We present efficient algorithms for testing the existence of a crossing-free leader layout that labels all sites and also for maximizing the number of labeled sites in a crossing-free leader layout. For two-sided boundary labeling with adjacent sides, we further show how to minimize the total leader length in a crossing-free layout.

Description: In this paper we consider the problem of the strict self-assembly of infinite fractals within tile self-assembly. In particular, we provide tile assembly algorithms for the assembly of a Sierpinski triangle and the discrete Sierpinski carpet within a class of models we term the h - handed assembly model ( h -HAM), which generalizes the 2-HAM to allow up to h assemblies to combine in a single assembly step. Despite substantial consideration, no purely growth self-assembly model has yet been shown to strictly assemble an infinite fractal without significant modification to the fractal shape. In this paper we not only achieve this, but in the case of the Sierpinski carpet are able to achieve it within the 2-HAM, one of the most well studied tile assembly models in the literature. Our specific results are as follows: We provide a 6-HAM construction for a Sierpinski triangle that works at scale factor 1, 30 tile types, and assembles the fractal in a near perfect way in which all intermediate assemblies are finite-sized iterations of the recursive fractal. We further assemble a Sierpinski triangle within the 3-HAM at scale factor 3 and 990 tile types. For the Sierpinski carpet, we present a 2-HAM result that works at scale factor 3 and uses 1216 tile types. We further include analysis showing that the aTAM is incapable of strictly assembling the Sierpinski triangle considered in this paper, and that multiple hands are needed for the near-perfect assembly of a Sierpinski triangle and the Sierpinski carpet.

Description: We consider k -Facility Location games, where n strategic agents report their locations on the real line and a mechanism maps them to k facilities. Each agent seeks to minimize his connection cost, given by a nonnegative increasing function of his distance to the nearest facility. Departing from previous work, that mostly considers the identity cost function, we are interested in mechanisms without payments that are (group) strategyproof for any given cost function, and achieve a good approximation ratio for the social cost and/or the maximum cost of the agents. We present a randomized mechanism, called Equal Cost , which is group strategyproof and achieves a bounded approximation ratio for all k and n , for any given concave cost function. The approximation ratio is at most 2 for Max Cost and at most n for Social Cost . To the best of our knowledge, this is the first mechanism with a bounded approximation ratio for instances with \(k \ge 3\) facilities and any number of agents. Our result implies an interesting separation between deterministic mechanisms, whose approximation ratio for Max Cost jumps from 2 to unbounded when k increases from 2 to 3, and randomized mechanisms, whose approximation ratio remains at most 2 for all k . On the negative side, we exclude the possibility of a mechanism with the properties of Equal Cost for strictly convex cost functions. We also present a randomized mechanism, called Pick the Loser , which applies to instances with k facilities and only \(n = k+1\) agents. For any given concave cost function, Pick the Loser is strongly group strategyproof and achieves an approximation ratio of 2 for Social Cost .

Description: We give a deterministic #SAT algorithm for de Morgan formulas of size up to \(n^{2.63}\) , which runs in time \(2^{n-n^{{\varOmega }(1)}}\) . This improves upon the deterministic #SAT algorithm of Chen et al. (Proceedings of the twenty-ninth annual IEEE conference on computational complexity, 2014 ), which has similar running time but works only for formulas of size less than \(n^{2.5}\) . Our new algorithm is based on the shrinkage of de Morgan formulas under random restrictions, shown by Paterson and Zwick (Random Struct Algorithms 4(2):135–150, 1993 ). We prove a concentrated and constructive version of their shrinkage result. Namely, we give a deterministic polynomial-time algorithm that selects variables in a given de Morgan formula so that, with high probability over the random assignments to the chosen variables, the original formula shrinks in size, when simplified using a given deterministic polynomial-time formula-simplification algorithm.

Description: We consider Conditional random fields ( CRFs ) with pattern-based potentials defined on a chain. In this model the energy of a string (labeling) \(x_1\ldots x_n\) is the sum of terms over intervals [ i ,  j ] where each term is non-zero only if the substring \(x_i\ldots x_j\) equals a prespecified pattern w . Such CRFs can be naturally applied to many sequence tagging problems. We present efficient algorithms for the three standard inference tasks in a CRF, namely computing (i) the partition function, (ii) marginals, and (iii) computing the MAP. Their complexities are respectively \(O(\textit{nL})\) , \(O(\textit{nL} \ell _{\max })\) and \(O(\textit{nL} \min \{|D|,\log (\ell _{\max }\!+\!1)\})\) where L is the combined length of input patterns, \(\ell _{\max }\) is the maximum length of a pattern, and D is the input alphabet. This improves on the previous algorithms of Ye et al. (NIPS, 2009 ) whose complexities are respectively \(O(\textit{nL} |D|)\) , \(O\left( n |\varGamma | L^2 \ell _{\max }^2\right) \) and \(O(\textit{nL} |D|)\) , where \(|\varGamma |\) is the number of input patterns. In addition, we give an efficient algorithm for sampling, and revisit the case of MAP with non-positive weights.

Description: Estimating the number of triangles in graph streams using a limited amount of memory has become a popular topic in the last decade. Different variations of the problem have been studied, depending on whether the graph edges are provided in an arbitrary order or as incidence lists. However, with a few exceptions, the algorithms have considered insert-only streams. We present a new algorithm estimating the number of triangles in dynamic graph streams where edges can be both inserted and deleted. We show that our algorithm achieves better time and space complexity than previous solutions for various graph classes, for example sparse graphs with a relatively small number of triangles. Also, for graphs with constant transitivity coefficient, a common situation in real graphs, this is the first algorithm achieving constant processing time per edge. The result is achieved by a novel approach combining sampling of vertex triples and sparsification of the input graph. In the course of the analysis of the algorithm we present a lower bound on the number of pairwise independent 2-paths in general graphs which might be of independent interest. At the end of the paper we discuss lower bounds on the space complexity of triangle counting algorithms that make no assumptions on the structure of the graph.

Description: During at-speed test of high performance sequential ICs using scan-based Logic BIST, the IC activity factor (AF) induced by the applied test vectors is significantly higher than that experienced during its in field operation. Consequently, power droop (PD) may take place during both shift and capture phases, which will slow down the circuit under test (CUT) signal transitions. At capture, this phenomenon is likely to be erroneously recognized as due to delay faults. As a result, a false test fail may be generated, with consequent increase in yield loss. In this paper, we propose two approaches to reduce the PD generated at capture during at-speed test of sequential circuits with scan-based Logic BIST using the Launch-On-Shift scheme. Both approaches increase the correlation between adjacent bits of the scan chains with respect to conventional scan-based LBIST. This way, the AF of the scan chains at capture is reduced. Consequently, the AF of the CUT at capture, thus the PD at capture, is also reduced compared to conventional scan-based LBIST. The former approach, hereinafter referred to as Low-Cost Approach (LCA), enables a 50 percent reduction in the worst case magnitude of PD during conventional logic BIST. It requires a small cost in terms of area overhead (of approximately 1.5 percent on average), and it does not increase the number of test vectors over the conventional scan-based LBIST to achieve the same Fault Coverage (FC). Moreover, compared to three recent alternative solutions, LCA features a comparable AF in the scan chains at capture, while requiring lower test time and area overhead. The second approach, hereinafter referred to as High-Reduction Approach (HRA), enables scalable PD reductions at capture of up to 87 percent, with limited additional costs in terms of area overhead and number of required test vectors for a given target FC, over our LCA approach. Particularly, compared to two of the three recent alternative solutions mentioned above, HRA en- bles a significantly lower AF in the scan chains during the application of test vectors, while requiring either a comparable area overhead or a significantly lower test time. Compared to the remaining alternative solutions mentioned above, HRA enables a similar AF in the scan chains at capture (approximately 90 percent lower than conventional scan-based LBIST), while requiring a significantly lower test time (approximately 4.87 times on average lower number of test vectors) and comparable area overhead (of approximately 1.9 percent on average).

Description: We consider the problems of finding optimal identifying codes, (open) locating-dominating sets and resolving sets (denoted Identifying Code , (Open) Open Locating-Dominating Set and Metric Dimension ) of an interval or a permutation graph. In these problems, one asks to distinguish all vertices of a graph by a subset of the vertices, using either the neighbourhood within the solution set or the distances to the solution vertices. Using a general reduction for this class of problems, we prove that the decision problems associated to these four notions are NP-complete, even for interval graphs of diameter 2 and permutation graphs of diameter 2. While Identifying Code and (Open) Locating-Dominating Set are trivially fixed-parameter-tractable when parameterized by solution size, it is known that in the same setting Metric Dimension is W [2]-hard. We show that for interval graphs, this parameterization of Metric Dimension is fixed-parameter-tractable.

Description: Given a partition of an n element set into equivalence classes, we study the problem of assigning unique labels to these elements in order to support the query that asks whether the elements corresponding to two given labels belong to the same equivalence class. This has various applications including for testing whether two vertices are in the same connected component in an undirected graph or in the same strongly connected component in a directed graph. We consider the problem in several models. Concerning labeling schemes where we assign labels to elements and the query is to be answered just by examining the labels of the queried elements (without any extra space): if each vertex is required to have a unique label, then we show that a label space of \(\sum _{i=1}^n \lfloor {n \over i} \rfloor \) is necessary and sufficient. In other words, \(\lg n + \lg \lg n + O(1)\) bits of space are necessary and sufficient for representing each of the labels. This slightly strengthens the known lower bound and is in contrast to the known necessary and sufficient bound of \(\lceil \lg n \rceil \) for the label length, if each vertex need not get a unique label. Concerning succinct data structures for the problem when the n elements are to be uniquely assigned labels from label set \(\{1,\ldots , n\}\) , we first show that \(\varTheta (\sqrt{n})\) bits are necessary and sufficient to represent the equivalence class information. This space includes the space for implicitly encoding the vertex labels. We can support the query in such a structure in O (1) time in the standard word RAM model. We also develop a dynamic structure that uses \(O(\sqrt{n} \lg n)\) bits to support equivalence queries and unions in \(O(\lg n/\lg \lg n)\) worst case time or \(O(\alpha (n))\) expected amortized time where \(\alpha (n)\) is the inverse Ackermann function. Concerning succinct data structures for the problem when the n elements are to be uniquely assigned labels from label set \(\{1,\ldots , cn\}\) for any constant \(c 〉 1\) , we show that \(\varTheta (\lg n)\) bits are necessary and sufficient to represent the equivalence class information. Moreover, we can support the query in such a structure in O (1) time in the standard word RAM model. We believe that our work can trigger further work on tradeoffs between label space and auxiliary data structure space for other labeling problems.

Description: We perform a thorough study of various characteristics of the asynchronous push–pull protocol for spreading a rumor on Erdős–Rényi random graphs \(G_{n,p}\) , for any \(p〉c\ln (n)/n\) with \(c〉1\) . In particular, we provide a simple strategy for analyzing the asynchronous push–pull protocol on arbitrary graph topologies and apply this strategy to \(G_{n,p}\) . We prove tight bounds of logarithmic order for the total time that is needed until the information has spread to all nodes. Surprisingly, the time required by the asynchronous push–pull protocol is asymptotically almost unaffected by the average degree of the graph. Similarly tight bounds for Erdős–Rényi random graphs have previously only been obtained for the synchronous push protocol, where it has been observed that the total running time increases significantly for sparse random graphs. Finally, we quantify the robustness of the protocol with respect to transmission and node failures. Our analysis suggests that the asynchronous protocols are particularly robust with respect to these failures compared to their synchronous counterparts.

Description: We study connectivity relations among points, where the precise location of each input point lies in a region of uncertainty. We distinguish two fundamental scenarios under which uncertainty arises. In the favorable Best-Case Uncertainty , each input point can be chosen from a given set to yield the best possible objective value. In the unfavorable Worst-Case Uncertainty , the input set has worst possible objective value among all possible point locations, which are uncertain due, for example, to imprecise data. We consider these notions of uncertainty for the bottleneck spanning tree problem, giving rise to the following Best-Case Connectivity with Uncertainty problem: given a family of geometric regions, choose one point per region, such that the longest edge length of an associated geometric spanning tree is minimized. We show that this problem is NP-hard even for very simple scenarios in which the regions are line segments or squares. On the other hand, we give an exact solution for the case in which there are \(n+k\) regions, where k of the regions are line segments and n of the regions are fixed points. We then give approximation algorithms for cases where the regions are either all line segments or all unit discs. We also provide approximation methods for the corresponding Worst-Case Connectivity with Uncertainty problem: Given a set of uncertainty regions, find the minimal distance r such that for any choice of points, one per region, there is a spanning tree among the points with edge length at most r .

Description: We define the modular treewidth of a graph as its treewidth after contraction of modules. This parameter properly generalizes treewidth and is itself properly generalized by clique-width. We show that the number of satisfying assignments can be computed in polynomial time for CNF formulas whose incidence graphs have bounded modular treewidth. Our result generalizes known results for the treewidth of incidence graphs and is incomparable with known results for clique-width (or rank-width) of signed incidence graphs. The contraction of modules is an effective data reduction procedure. Our algorithm is the first one to harness this technique for #SAT. The order of the polynomial bounding the runtime of our algorithm depends on the modular treewidth of the input formula. We show that it is unlikely that this dependency can be avoided by proving that SAT is W[1]-hard when parameterized by the modular incidence treewidth of the given CNF formula.

Description: In a classical online network design problem, traffic requirements are gradually revealed to an algorithm. Each time a new request arrives, the algorithm has to satisfy it by augmenting the network under construction in a proper way (with no possibility of recovery). In this paper we study a natural generalization of online network design problems, where a fraction of the requests (the outliers ) can be disregarded. Now, each time a request arrives, the algorithm first decides whether to satisfy it or not, and only in the first case it acts accordingly. We cast three classical network design problems into this framework: (i) Online Steiner tree with outliers In this case a set of t terminals that belong to an n -node graph is presented, one at a time, to an algorithm. Each time a new terminal arrives, the algorithm can either discard or select it. In the latter case, the algorithm connects it to the Steiner tree under construction (initially consisting of a given root node). At the end of the process, at least k terminals must be selected. (ii) Online TSP with outliers This is the same problem as above, but with the Steiner tree replaced by a TSP tour. (iii) Online facility location with outliers In this case, we are also given a set of facility nodes, each one with an opening cost. Each time a terminal is selected, we have to connect it to some facility (and open that facility, if it is not already open). We focus on the known distribution model, where terminals are independently sampled from a given distribution. For all the above problems, we present bicriteria online algorithms that, for any constant \(\epsilon 〉0\) , select at least \((1-\epsilon )k\) terminals with high probability and pay in expectation \(O(\log ^2n)\) times more than the expected cost of the optimal offline solution (selecting k terminals). These upper bounds are complemented by inapproximability results for the case that one insists on selecting exactly k terminals, and by lower bounds including an \(\varOmega (\log n/\log \log n)\) lower bound for the case that the online algorithm is allowed to select \(\alpha \,k\) terminals only, for a sufficiently large constant \(\alpha \in (0,1)\) .

Description: A well known result in graph algorithms, due to Edmonds, states that given a digraph D and a positive integer \(\ell \) , we can test whether D contains \(\ell \) arc-disjoint out-branchings in polynomial time. However, if we ask whether there exists an out-branching and an in-branching which are arc-disjoint, then the problem becomes NP -complete. In fact, even deciding whether a digraph D contains an out-branching which is arc-disjoint from some spanning tree in the underlying undirected graph remains NP -complete. In this paper we formulate some natural optimization questions around these problems and initiate its study in the realm of parameterized complexity. More precisely, the problems we study are the following: Arc - Disjoint Branchings and Non - Disconnecting Out - Branching . In Arc - Disjoint Branchings ( Non - Disconnecting Out - Branching ), a digraph D and a positive integer k are given as input and the goal is to test whether there exist an out-branching and in-branching (respectively, a spanning tree in the underlying undirected graph) that differ on at least k arcs. We obtain the following results for these problems. Non - Disconnecting Out - Branching is fixed parameter tractable (FPT) and admits a linear vertex kernel. Arc - Disjoint Branchings is FPT on strong digraphs. The algorithm for Non - Disconnecting Out - Branching runs in time \(2^{\mathcal {O}(k)}n^{\mathcal {O}(1)}\) and the approach we use to obtain this algorithms seems useful in designing other moderately exponential time algorithms for edge/arc partitioning problems.

Description: We study the stable roommates problem in networks where players are embedded in a social context and may incorporate positive externalities into their decisions. Each player is a node in a social network and strives to form a good match with a neighboring player. We consider the existence, computation, and inefficiency of stable matchings from which no pair of players wants to deviate. We characterize prices of anarchy and stability, which capture the ratio of the total profit in the optimum matching over the total profit of the worst and best stable matching, respectively. When the benefit from a match (which we model by associating a reward with each edge) is the same for both players, we show that externalities can significantly improve the price of stability, while the price of anarchy remains unaffected. Furthermore, a good stable matching achieving the bound on the price of stability can be obtained in polynomial time. We extend these results to more general matching rewards, when players matched to each other may receive different benefits from the match. For this more general case, we show that network externalities (i.e., “caring about your friends”) can make an even larger difference and greatly reduce the price of anarchy. We show a variety of existence results and present upper and lower bounds on the prices of anarchy and stability for various structures of matching benefits. All our results on stable matchings immediately extend to the more general case of fractional stable matchings.

Description: We present the first general bounds on the mixing time of the Markov chain associated to the logit dynamics for wide classes of strategic games. The logit dynamics with inverse noise \(\beta \) describes the behavior of a complex system whose individual components act selfishly according to some partial (“noisy”) knowledge of the system, where the capacity of the agent to know the system and compute her best move is measured by parameter \(\beta \) . In particular, we prove nearly tight bounds for potential games and games with dominant strategies. Our results show that for potential games the mixing time is bounded by an exponential in \(\beta \) and in the maximum potential difference. Instead, for games with dominant strategies the mixing time cannot grow arbitrarily with \(\beta \) . Finally, we refine our analysis for a subclass of potential games called graphical coordination games, often used for modeling the diffusion of new technologies. We prove that the mixing time of the logit dynamics for these games can be upper bounded by a function that is exponential in the cutwidth of the underlying graph and in \(\beta \) . Moreover, we consider two specific and popular network topologies, the clique and the ring. For the clique, we prove an almost matching lower bound on the mixing time of the logit dynamics that is exponential in \(\beta \) and in the maximum potential difference, while for the ring we prove that the time of convergence of the logit dynamics to its stationary distribution is significantly shorter.

Description: Given a plane graph G (i.e., a planar graph with a fixed planar embedding and outer face) and a biconnected subgraph \(G^{\prime }\) with a fixed planar straight-line convex drawing, we consider the question whether this drawing can be extended to a planar straight-line drawing of G . We characterize when this is possible in terms of simple necessary conditions, which we prove to be sufficient. This also leads to a linear-time testing algorithm. If a drawing extension exists, one can be computed in the same running time.

Description: The advent of the cloud computing makes storage outsourcing become a rising trend, which promotes the secure remote data auditing a hot topic that appeared in the research literature. Recently some research consider the problem of secure and efficient public data integrity auditing for shared dynamic data. However, these schemes are still not secure against the collusion of cloud storage server and revoked group users during user revocation in practical cloud storage system. In this paper, we figure out the collusion attack in the exiting scheme and provide an efficient public integrity auditing scheme with secure group user revocation based on vector commitment and verifier-local revocation group signature. We design a concrete scheme based on the our scheme definition. Our scheme supports the public checking and efficient user revocation and also some nice properties, such as confidently, efficiency, countability and traceability of secure group user revocation. Finally, the security and experimental analysis show that, compared with its relevant schemes our scheme is also secure and efficient.

Description: To select an appropriate level of error protection in caches, the impact of various protection schemes on the cache Failure In Time (FIT) rate must be evaluated for a target benchmark suite. However, while many simulation tools exist to evaluate area, power and performance for a set of benchmark programs, there is a dearth of such tools for reliability. This paper introduces a new cache reliability model called PARMA+ that has unique features which distinguish it from previous models. PARMA+ estimates a cache's FIT rate in the presence of spatial multi-bit faults, single-bit faults, temporal multi-bit faults and different error protection schemes including parity, ECC, early write-back and bit-interleaving. We first develop the model formally, then we demonstrate its accuracy. We have run reliability simulations for many distributions of large and small fault patterns and have compared them with accelerated fault injection simulations. PARMA+ has high accuracy and low computational complexity.

Description: Although the travel time is the most important information in road networks, many spatial queries, e.g., $k$ -nearest-neighbor ( $k$ -NN) and range queries, for location-based services (LBS) are only based on the network distance. This is because it is costly for an LBS provider to collect real-time traffic data from vehicles or roadside sensors to compute the travel time between two locations. With the advance of web mapping services, e.g., Google Maps, Microsoft Bing Maps, and MapQuest Maps, there is an invaluable opportunity for using such services for processing spatial queries based on the travel time. In this paper, we propose a server-side S patial M ashup S ervice (SMS) that enables the LBS provider to efficiently evaluate $k$ -NN queries in road networks using the route information and travel time retrieved from an external web mapping service. Due to the high cost of retrieving such external information, the usage limits of web mapping services, and the large number of spatial queries, we optimize the SMS for a large number of $k$ -NN queries. We first discuss how the SMS processes a single $k$ -NN query using two optimizations, namely, direction sharing and parallel requesting . Then, we extend them to process multiple concurrent $k$ -NN queries and design a performance tuning tool to provide a trade-off between the query response time and the number of external requests and more importantly, to prevent a starvation problem in the parallel requesting optimization for concurrent queries. We evaluate the performance of the proposed SMS using MapQuest Maps, a real road network, real and synthetic data sets. Experimental results show the efficiency and scalability of our optimizations designed for the SMS.