Flexible Variant Research Articles

Cyvcf2: fast, flexible variant analysis with Python.

MotivationVariant call format (VCF) files document the genetic variation observed after DNA sequencing, alignment and variant calling of a sample cohort. Given the complexity of the VCF format as well as the diverse variant annotations and genotype metadata, there is a need for fast, flexible methods enabling intuitive analysis of the variant data within VCF and BCF files.ResultsWe introduce cyvcf2, a Python library and software package for fast parsing and querying of VCF and BCF files and illustrate its speed, simplicity and utility.Availability and Implementation cyvcf2 is available from https://github.com/brentp/cyvcf2 under the MIT license and from common python package managers. Detailed documentation is available at http://brentp.github.io/cyvcf2/

Standoff Photoacoustic Spectroscopy of Explosives.

Detection and identification of unknown and possibly hazardous materials is a vital area of research to which infrared (IR) spectroscopy is ideally suited. Infrared absorption spectra can be measured with many sensing paradigms of which photoacoustic spectroscopy (PAS) is a sensitive and flexible variant. The flexibility of PAS allows for the construction of narrowly tailored spectroscopic sensors that are designed for specific tasks. We discuss the evaluation of an interferometric PAS sensor by the measurement of common explosive hazards from a standoff distance of 1 m. Reproduction of IR absorption spectra for 1,3,5-trinitroperhydro-1,3,5-triazine (RDX), pentaerythritol tetranitrate (PETN), and 2,4,6-trinitrotoluene (TNT) demonstrate the capabilities of the interferometric sensor for standoff explosives detection.

Adaptive differential search algorithm for optimal location of distributed generation in the presence of SVC for power loss reduction in distribution system

Optimal location and sizing of multi type of distribution generations in a distribution system is of great importance for experts and industries to achieve the desired technical-economic objectives. This paper aims to develop a new planning strategy for modern power distribution system using a flexible variant based differential search (DS) algorithm named adaptive DS. The proposed algorithm investigated for solving the optimal location and sizing of multi distributed generation (DG). The total power losses have been optimized considering the cost component of DG for real power, and the cost of energy losses. The robustness of the proposed planning strategy was validated on a two practical test system, 33-Bus and 69 Bus at normal situation and considering specific loading margin stability. The results show the importance of installing the suitable size of DG at the suitable location in the presence of SVC compensators.

Percolation phase diagrams for multi-phase models built on the overlapping sphere model

The overlapping sphere (OS) percolation model gives a two-phase microstructure (matrix plus inclusions) that is useful for testing composite material ideas and other applications, as well as serving as a paradigm of overlapping object percolation and phase transitions. Real materials often have more than two phases, so it is of interest to extend the applicability of the OS model. A flexible variant of the OS model can be constructed by randomly assigning the spheres different phase labels, according to a uniform probability distribution, as they are inserted one by one into the matrix. The resulting three or more phase models can have different amounts of percolating and non-percolating phases, depending on the volume fraction of each phase and the total OS volume fraction. A three-dimensional digital image approach is used to approximately map out the percolation phase diagram of such models, explicitly up to four phases (one matrix plus three spherical inclusion phases) and implicitly for N>4 phases. For the three phase model, it was found that a single OS sub-phase has a percolation threshold that ranges from about a volume fraction of 0.16, when the matrix volume fraction is about 0.01, to about 0.30, at a matrix volume fraction of about 0.7. The approximate analytical dependence of this sub-phase percolation threshold on the defining model parameters serves to guide the building of the percolation phase diagram for the N-phase model, and is used to determine the maximum value of N(N=6) at which all N phases can be simultaneously percolated.

Flexible exponential integration methods for large systems of differential equations

In this paper, we describe a flexible variant of exponential integration methods for large systems of differential equations. This version possesses the flexibility and generality which allows to further exploit the special structure of the system. By using modified B-series and bi-coloured rooted trees, we can derive the general structure of the classical order conditions for these schemes. Some numerical schemes are constructed and the order conditions are derived. Numerical experiments with reaction-diffusion type problems are included.

Customizable Point-of-Interest Queries in Road Networks

We present a unified framework for dealing with exact point-of-interest (POI) queries in dynamic continental road networks within interactive applications. We show that partition-based algorithms developed for point-to-point shortest path computations can be naturally extended to handle augmented queries such as finding the closest restaurant or the best post office to stop on the way home, always ranking POIs according to a user-defined cost function. Our solution allows different trade-offs between indexing effort (time and space) and query time. Our most flexible variant allows the road network to change frequently (to account for traffic information or personalized cost functions) and the set of POIs to be specified at query time. Even in this fully dynamic scenario, our solution is fast enough for interactive applications on continental road networks.

Screening smartphone applications using malware family signatures

The sharp increase in smartphone malware has become one of the most serious security problems. Since the Android platform has taken the dominant position in smartphone popularity, the number of Android malware has grown correspondingly and represents critical threat to the smartphone users. This rise in malware is primarily attributable to the occurrence of variants of existing malware. A set of variants stem from one malware can be considered as one malware family, and malware families cover more than half of the Android malware population. A conventional technique for defeating malware is the use of signature matching which is efficient from a time perspective but not very practical because of its lack of robustness against the malware variants. As a counter approach for handling the issue of variants behavior analysis techniques have been proposed but require extensive time and resources. In this paper, we propose an Android malware detection mechanism that uses automated family signature extraction and family signature matching. Key concept of the mechanism is to extract a set of family representative binary patterns from evaluated family members as a signature and to classify each set of variants into a malware family via an estimation of similarity to the signatures. The proposed family signature and detection mechanism offers more flexible variant detection than does the legacy signature matching, which is strictly dependent on the presence of a specific string. Furthermore, compared with the previous behavior analysis techniques considering family detection, the proposed family signature has higher detection accuracy without the need for the significant overhead of data and control flow analysis. Using the proposed signature, we can detect new variants of known malware efficiently and accurately by static matching. We evaluated our mechanism with 5846 real world Android malware samples belonging to 48 families collected in April 2014 at an anti-virus company; experimental results showed that; our mechanism achieved greater than 97% accuracy in detection of variants. We also demonstrated that the mechanism has a linear time complexity with the number of target applications.

Pediatric flatfoot

The current review includes the most up to date literature on the cause, epidemiology, diagnosis, and treatment of pediatric flatfeet. Recent systematic reviews concur that the evidence supporting the use of orthotics in pediatric flexible flatfeet is poor. Multiple studies have recently reported on the results of arthroereisis, yet these are mostly retrospective and do not include a comparative group or long-term follow up. Other options for symptomatic flatfeet may include osteotomies and/or fusions, but similarly high quality comparative studies are lacking. Pediatric flatfeet range from the painless flexible normal variant of growth, to stiff or painful manifestations of tarsal coalition, collagen abnormalities, neurologic disease, or other underlying condition. Most children with flexible flatfeet do not have symptoms and do not require treatment. In symptomatic children, orthotics, osteotomies, or fusions may be considered. Arthroereisis has gained popularity in Europe, but has not been widely adopted in North America. Children with asymptomatic rigid flatfeet may not require treatment, whereas those with pain or functional deficits may benefit from orthotics, osteotomies, or fusions. A careful history, clinical exam, and selective diagnostic testing can be used to determine the appropriate treatment option for each child.

A block [formula omitted] method for linear systems with multiple right-hand sides

This study is mainly focused on iterative solution to multiple linear systems with several right-hand sides. For solving such systems efficiently, we explore a new block GCROT(m,k) (BGCROT(m,k)) method, which is derived by extending GCROT(m,k) method [Jason E. Hicken, David W. Zingg, A simplified and flexible variant of GCROT for solving nonsymmetric linear systems, SIAM J. Sci. Comput. 32 (2010) 1672–1694]. We analyze its main properties. It is shown that under the condition of full rank of block residual, the Frobenius norm of the block residual generated by the proposed method is always nonincreasing. Moreover, we also present its block flexible version, BFGCROT(m,k). Finally, numerical examples demonstrate that the BGCROT(m,k) method and its flexible variant can achieve a smoothed residual and can be more competitive than some other block solvers.

Online Clustering on the Line with Square Cost Variable Sized Clusters

In the online clustering problems, the classification of points into sets (called clusters) is done in an online fashion. Points arrive one by one at arbitrary locations, to be assigned to clusters at the time of arrival without any information about the further points. A point can be assigned to an existing cluster, or a new cluster can be opened for it. Existing clusters cannot be merged or split. We study one-dimensional variants. The cost of a cluster is the sum of a fixed setup cost scaled to 1 and the square of the diameter of the cluster. The goal is to minimize the sum of costs of the clusters used by the algorithm. In this paper we investigate the problem on the line. We examine two versions, both maintaining the properties that a point which was assigned to a given cluster must remain assigned to this cluster, and clusters cannot be merged. In the strict variant, the size and the exact location of the cluster must be fixed when it is initialized. In the flexible variant, the algorithm can shift the cluster or expand it, as long as it contains all points assigned to it. We consider the online and the semi-online (the input is sorted according to their coordinates from smallest to largest i.e., from left to right) versions of the above two variants. We present the first online algorithms for the solution of the problem. We describe algorithms for the strict and the flexible variant both for the online and semi-online versions. We also give lower bounds on the possible competitive ratio in all of the cases.

OpenQFlow: Scalable OpenFlow with Flow-Based QoS

SUMMARY OpenFlow, originally proposed for campus and enterprise network experimentation, has become a promising SDN architecture that is considered as a widely-deployable production network node recently. It is, in a consequence, pointed out that OpenFlow cannot scale and replace today’s versatile network devices due to its limited scalability and flexibility. In this paper, we propose OpenQFlow, a novel scalable and flexible variant of OpenFlow. OpenQFlow provides a fine-grained flow tracking while flow classification is decoupled from the tracking by separating the inefficiently coupled flow table to three different tables: flow state table, forwarding rule table, and QoS rule table. We also develop a two-tier flowbased QoS framework, derived from our new packet scheduling algorithm, which provides performance guarantee and fairness on both granularity levels of micro- and aggregate-flow at the same time. We have implemented OpenQFlow on an off-the-shelf microTCA chassis equipped with a commodity multicore processor, for which our architecture is suited, to achieve high-performance with carefully engineered software design and optimiza

Optimization methodology based on neural networks and self-adaptive differential evolution algorithm applied to an aerobic fermentation process

The determination of the optimal neural network topology is an important aspect when using neural models. Due to the lack of consistent rules, this is a difficult problem, which is solved in this paper using an evolutionary algorithm namely Differential Evolution. An improved, simple, and flexible self-adaptive variant of Differential Evolution algorithm is proposed and tested. The algorithm included two initialization strategies (normal distribution and normal distribution combined with the opposition based principle) and a modified mutation principle. Because the methodology contains new elements, a specific name has been assigned, SADE-NN-1. In order to determine the most influential inputs of the models, a sensitivity analysis was applied. The case study considered in this work refer to the oxygen mass transfer coefficient in stirred bioreactors in the presence of n-dodecane as oxygen vector. The oxygen transfer in the fermentation broths has a significant influence on the growth of cultivated microorganism, the accurate modeling of this process being an important problem that has to be solved in order to optimize the aerobic fermentation process.The neural networks predicted the mass transfer coefficients with high accuracy, which indicates that the proposed methodology had a good performance. The same methodology, with a few modifications, and with the best neural network models, was used for determining the optimal conditions for which the mass transfer coefficient is maximized.A short review of the differential evolution methodology is realized in the first part of this article, presenting the main characteristics and variants, with advantages and disadvantages, and fitting in the modifications proposed within the existing directions of research.

Flexible Variants of Block Restarted GMRES Methods with Application to Geophysics

In a wide number of applications in computational science and engineering the solution of large linear systems of equations with several right-hand sides given at once is required. Direct methods based on Gaussian elimination are known to be especially appealing in that setting. Nevertheless, when the dimension of the problem is very large, preconditioned block Krylov space solvers are often considered as the method of choice. The purpose of this paper is thus to present iterative methods based on block restarted GMRES that allow variable preconditioning for the solution of linear systems with multiple right-hand sides. The use of flexible methods is especially of interest when approximate possibly iterative solvers are considered in the preconditioning phase. First we introduce a new variant of block flexible restarted GMRES that includes a strategy for detecting when a linear combination of the systems has approximately converged. This explicit block size reduction is often called deflation. We analyze the main properties of this flexible method based on deflation and notably prove that the Frobenius norm of the block residual is always nonincreasing. We also present a flexible variant based on both deflation and truncation to especially be used in case of limited memory. Finally we illustrate the numerical behavior of these flexible block methods for large industrial simulations arising in geophysics, where indefinite linear systems of size up to 1 billion unknowns with multiple right-hand sides have been successfully solved in a parallel distributed memory environment.

Magneto-inductive cable arrays: Estimation and reduction of crosstalk

Magneto-inductive waveguides are linear periodic structures consisting of regular arrangements of L-C resonators coupled together by mutual inductances M. Magneto-inductive cable is a low-loss flexible variant, based on overlapping inductors and parallel plate capacitors formed by double-sided patterning of copper-clad polyimide. The properties of cable arrays formed from a set of parallel magneto-inductive lines are investigated. Numerical solutions are provided for typical arrangements. Analytic methods are introduced for estimating the coupling between elements in neighboring cables and the frequency dependence of cross-talk. Theoretical confirmation is provided by experimental results for cables operating at ≈100 MHz. Strategies for reducing cross-talk using alternative element designs that achieve low mutual inductance by cancellation of induced currents are explored.

Operator‐based interpolation for bootstrap algebraic multigrid

AbstractBootstrap algebraic multigrid (BAMG) is a multigrid‐based solver for matrix equations of the form Ax=b. Its aim is to automatically determine the interpolation weights used in algebraic multigrid (AMG) by locally fitting a set of test vectors that have been relaxed as solutions to the corresponding homogeneous equation, Ax=0, and are then possibly improved later using a multilevel eigensolver. This paper introduces a flexible variant of BAMG that determines the interpolation weights indirectly by ‘collapsing’ the unwanted connections in ‘operator interpolation’. Compared to BAMG, this indirect BAMG approach (iBAMG) is more in the spirit of classical AMG, which collapses unwanted connections in operator interpolation based on the (restrictive) assumption that smooth error is locally constant. This paper studies the numerical performance of iBAMG and establishes an equivalence, under certain assumptions, between it and a slightly modified (standard) BAMG scheme. To focus on camparing BAMG and iBAMG and exposing their behavior as the problem size grows, the numerical experiments concentrate on Poisson‐like scalar problems. Copyright © 2010 John Wiley & Sons, Ltd.

A Simplified and Flexible Variant of GCROT for Solving Nonsymmetric Linear Systems

There is a need for flexible iterative solvers that can solve large-scale ($>10^6$ unknowns) nonsymmetric sparse linear systems to a small tolerance. Among flexible solvers, flexible GMRES (FGMRES) is attractive because it minimizes the residual norm over a particular subspace. In practice, FGMRES is often restarted periodically to keep memory and work requirements reasonable; however, like restarted GMRES, restarted FGMRES can suffer from stagnation. This has led us to develop a flexible variant of the Krylov linear solver GCROT (generalized conjugate residual with inner orthogonalization and outer truncation). Unlike the original GCROT algorithm, the proposed GCROT variant uses a simplified truncation strategy similar to loose GMRES (LGMRES). This modification is motivated by numerical experiments that suggest the specific subspace retained in the outer iteration of GCROT is less important than its size. The flexible GCROT variant appears to be well suited for advection-dominated problems. In particular, when applied to an adjoint problem from computational aerodynamics, the proposed GCROT variant is robust and efficient compared with several popular truncated Krylov subspace methods. Finally, a flexible version of LGMRES is easily constructed by recognizing algorithmic similarities to GCROT.

Algebraic Multigrid Based on Computational Molecules, 2: Linear Elasticity Problems

This paper deals with a new approach in algebraic multigrid (AMG) for self-adjoint and elliptic problems arising from finite-element discretization of linear elasticity problems. Generalizing our approach for scalar problems [J. K. Kraus and J. Schicho, Computing, 77 (2006), pp. 57–75], we propose an edge-matrix concept for point-block systems of linear algebraic equations. This gives a simple and reliable method for the evaluation of the strength of nodal dependence that can be applied to symmetric positive definite non-M matrices. In this paper the edge-matrix concept is developed for and applied to (two- as well as three-dimensional) linear elasticity problems. We consider approximate splittings of the problem-related element matrices into symmetric positive semidefinite edge matrices of rank one. The reproduction of edge matrices on coarse levels offers the opportunity to combine classical coarsening techniques with robust (energy-minimizing) interpolation schemes: The “computational molecules” involved in this process are assembled from edge matrices. This yields a flexible new variant of AMG that allows also for an efficient solution of problems with discontinuous coefficients, e.g., for composite materials.

Numerical experiments on a flexible variant of GMRES‐DR

AbstractThe Flexible GMRES (FGMRES [1]) and the GMRES with deflated restarting (GMRES‐DR [2]) methods are two algorithms derived from GMRES [3], that are considered as powerful when solving large non hermitian systems of linear equations. GMRES‐DR is a variant of GMRES with an improved restarting technique that maintains in the Krylov subspace harmonic Ritz vector from the previous restart. In situations where the convergence of restarted GMRES is slow and where the matrix has few eigenvalues close to the origin, this technique has proved very efficient. The new method that we propose is the Flexible GMRES with deflated restarting (FGMRES‐DR [6]), which combines the two above mentioned algorithms in order to yield better performance. (© 2008 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)

Rigidification of a Flexible Protease Inhibitor Variant upon Binding to Trypsin

The Tyr35 → Gly replacement in bovine pancreatic trypsin inhibitor (BPTI) has previously been shown to dramatically enhance the flexibility of the trypsin-binding region of the free inhibitor and to destabilize the interaction with the protease by about 3 kcal/mol. The effects of this replacement on the enzyme-inhibitor interaction were further studied here by X-ray crystallography and isothermal titration calorimetry (ITC). The co-crystal structure of Y35G BPTI bound to trypsin was determined using 1.65 Å resolution X-ray diffraction data collected from cryopreserved crystals, and a new structure of the complex with wild-type BPTI under the same conditions was determined using 1.62 Å data. These structures reveal that, in contrast to the free protein, Y35G BPTI adopts a conformation nearly identical with that of the wild-type protein, with a water-filled cavity in place of the missing Tyr side-chain. The crystallographic temperature factors for the two complexes indicate that the mutant inhibitor is nearly as rigid as the wild-type protein when bound to trypsin. Calorimetric measurements show that the change in enthalpy upon dissociation of the complex is 2.5 kcal/mol less favorable for the complex containing Y35G BPTI than for the complex with the wild-type inhibitor. Thus, the destabilization of the complex resulting from the Y35G replacement is due to a more favorable change in entropy upon dissociation. The heat capacity changes for dissociation of the mutant and wild-type complexes were very similar, suggesting that the entropic effects probably do not arise from solvation effects, but are more likely due to an increase in protein conformational entropy upon dissociation of the mutant inhibitor. These results define the biophysical role of a highly conserved core residue located outside of a protein-binding interface, demonstrating that Tyr35 has little impact on the trypsin-bound BPTI structure and acts primarily to define the structure of the free protein so as to maximize binding affinity.

Variations on a Theme Called PACE

The Program for All-inclusive Care of the Elderly (PACE) has been hailed as successful but of limited appeal. This study contrasts the effects on hospital utilization of PACE and a more liberal variant, the Wisconsin Partnership Program (WPP). Hospital and emergency room (ER) utilization data from two sites that used both PACE and WPP to serve elderly clients were compared. The analysis of utilization was conducted using a cross-sectional longitudinal approach. The statistical significance of the difference between WPP and PACE groups was calculated by using regressions that adjusted for gender, race (white/nonwhite), age, original reason for entitlement in Medicare (elderly/disabled), dual eligibility, diagnoses during the previous 6 months, and county of residence. The PACE enrollees had fewer hospital admissions, preventable hospital admissions, hospital days, ER visits, and preventable ER visits than the WPP enrollees had. There was no difference in the length of hospital stays. PACE is more effective in controlling hospital and ER utilization than is the more flexible variant (WPP).