arXiv subjects

Kapil Ahuja

Publications and source records attributed to Kapil Ahuja.

33 records · Page 2Linked to original sources

arXiv2018

Vector Quantized Spectral Clustering applied to Soybean Whole Genome Sequences

We develop a Vector Quantized Spectral Clustering (VQSC) algorithm that is a combination of Spectral Clustering (SC) and Vector Quantization (VQ) sampling for grouping Soybean genomes. The inspiration here is to use SC for its accuracy and VQ to make the algorithm computationally cheap (the complexity of SC is cubic in-terms of the input size). Although the combination of SC and VQ is not new, the novelty of our work is in developing the crucial similarity matrix in SC as well as use of k-medoids in VQ, both adapted for the Soybean genome data. We compare our approach with commonly used techniques like UPGMA (Un-weighted Pair Graph Method with Arithmetic Mean) and NJ (Neighbour Joining). Experimental results show that our approach outperforms both these techniques significantly in terms of cluster quality (up to 25% better cluster quality) and time complexity (order of magnitude faster).

q-bio.QM↗

arXiv2018

Preconditioned Linear Solves for Parametric Model Order Reduction

The main computational cost of algorithms for computing reduced-order models of parametric dynamical systems is in solving sequences of very large and sparse linear systems. We focus on efficiently solving these linear systems, arising while reducing second-order linear dynamical systems, by iterative methods with appropriate preconditioners. We propose that the choice of underlying iterative solver is problem dependent. We propose the use of block variant of the underlying iterative method because often all right-hand-side are available together. Since, Sparse Approximate Inverse (SPAI) preconditioner is a general preconditioner that can be naturally parallelized, we propose its use. Our most novel contribution is a technique to cheaply update the SPAI preconditioner, while solving the parametrically changing linear systems. We support our proposed theory by numerical experiments where we first show benefit of 80% in time by using a block iterative method, and a benefit of 70% in time by using SPAI updates.

math.NA↗

arXiv2018

Parallel FPGA Router using Sub-Gradient method and Steiner tree

In the FPGA (Field Programmable Gate Arrays) design flow, one of the most time-consuming step is the routing of nets. Therefore, there is a need to accelerate it. In a recent paper by Hoo et. al., the authors have developed a Linear Programming based framework that parallelizes this routing process to achieve significant speedups (the algorithm is termed as ParaLaR). However, this approach has certain weaknesses. Namely, the constraints violation by the solution and a local minima that could be improved. We address these two issues here. In our paper, we use this framework and solve it using the Primal-Dual sub-gradient method that better exploits the problem properties. We also propose a better way to update the size of the step taken by this iterative algorithm. We perform experiments on a set of standard benchmarks, where we show that our algorithm outperforms the standard existing algorithms (VPR and ParaLaR). We achieve up to 22% improvement in the constraints violation and the standard metric of the minimum channel width when compared with ParaLaR (which is same as in VPR). We achieve about 20% savings in another standard metric of the total wire length (when compared with VPR), which is the same as for ParaLaR. Hence, our algorithm achieves minimum value for all the three parameters. Also, the critical path delay for our algorithm is almost same as compared to VPR and ParaLaR. We achieve relative speedups of 3 times when we run a parallel version of our algorithm using 4 threads.

cs.DC↗

arXiv2018

Localized Multiple Kernel Learning for Anomaly Detection: One-class Classification

Multi-kernel learning has been well explored in the recent past and has exhibited promising outcomes for multi-class classification and regression tasks. In this paper, we present a multiple kernel learning approach for the One-class Classification (OCC) task and employ it for anomaly detection. Recently, the basic multi-kernel approach has been proposed to solve the OCC problem, which is simply a convex combination of different kernels with equal weights. This paper proposes a Localized Multiple Kernel learning approach for Anomaly Detection (LMKAD) using OCC, where the weight for each kernel is assigned locally. Proposed LMKAD approach adapts the weight for each kernel using a gating function. The parameters of the gating function and one-class classifier are optimized simultaneously through a two-step optimization process. We present the empirical results of the performance of LMKAD on 25 benchmark datasets from various disciplines. This performance is evaluated against existing Multi Kernel Anomaly Detection (MKAD) algorithm, and four other existing kernel-based one-class classifiers to showcase the credibility of our approach. Our algorithm achieves significantly better Gmean scores while using a lesser number of support vectors compared to MKAD. Friedman test is also performed to verify the statistical significance of the results claimed in this paper.

cs.LG↗

arXiv2018

Stability, Efficiency, and Contentedness of Social Storage Networks

Social storage systems are a good alternative to existing data backup systems of local, centralized, and P2P backup. In this paper, we look at two untouched aspects of social storage systems. One aspect involves modelling social storage as an endogenous social network, where agents themselves decide with whom they want to build data backup relation. The second aspect involves studying the stability of social storage systems, which would help reduce maintenance costs and further, help build efficient as well as contented networks. We have a four fold contribution that covers the above two aspects. We, first, model the social storage system as a strategic network formation game. We define the utility of each agent in the network under two different frameworks. Second, we propose the concept of bilateral stability which refines the pairwise stability concept defined by Jackson et. al. 1996, by requiring mutual consent for both addition and deletion of links, as compared to mutual consent just for link addition. Mutual consent for link deletion is especially important in the social storage setting. Third, we prove necessary and the sufficient conditions for bilateral stability of social storage networks. For symmetric social storage networks, we prove that there exists a unique neighborhood size, independent of the number of agents (for all non-trivial cases), where no pair of agents has any incentive to increase or decrease their neighborhood size. We call this neighborhood size as the stability point. Fourth, given the number of agents and other parameters, we discuss which bilaterally stable networks would evolve and also discuss which of these stable networks are efficient --- that is, stable networks with maximum sum of utilities of all agents. We also discuss ways to build contented networks, where each agent achieves the maximum possible utility.

cs.GT↗

arXiv2018

Online Learning with Regularized Kernel for One-class Classification

This paper presents an online learning with regularized kernel based one-class extreme learning machine (ELM) classifier and is referred as online RK-OC-ELM. The baseline kernel hyperplane model considers whole data in a single chunk with regularized ELM approach for offline learning in case of one-class classification (OCC). Further, the basic hyper plane model is adapted in an online fashion from stream of training samples in this paper. Two frameworks viz., boundary and reconstruction are presented to detect the target class in online RKOC-ELM. Boundary framework based one-class classifier consists of single node output architecture and classifier endeavors to approximate all data to any real number. However, one-class classifier based on reconstruction framework is an autoencoder architecture, where output nodes are identical to input nodes and classifier endeavor to reconstruct input layer at the output layer. Both these frameworks employ regularized kernel ELM based online learning and consistency based model selection has been employed to select learning algorithm parameters. The performance of online RK-OC-ELM has been evaluated on standard benchmark datasets as well as on artificial datasets and the results are compared with existing state-of-the art one-class classifiers. The results indicate that the online learning one-class classifier is slightly better or same as batch learning based approaches. As, base classifier used for the proposed classifiers are based on the ELM, hence, proposed classifiers would also inherit the benefit of the base classifier i.e. it will perform faster computation compared to traditional autoencoder based one-class classifier.

cs.LG↗

arXiv2018

Density-Wise Two Stage Mammogram Classification using Texture Exploiting Descriptors

Breast cancer is becoming pervasive with each passing day. Hence, its early detection is a big step in saving the life of any patient. Mammography is a common tool in breast cancer diagnosis. The most important step here is classification of mammogram patches as normal-abnormal and benign-malignant. Texture of a breast in a mammogram patch plays a significant role in these classifications. We propose a variation of Histogram of Gradients (HOG) and Gabor filter combination called Histogram of Oriented Texture (HOT) that exploits this fact. We also revisit the Pass Band - Discrete Cosine Transform (PB-DCT) descriptor that captures texture information well. All features of a mammogram patch may not be useful. Hence, we apply a feature selection technique called Discrimination Potentiality (DP). Our resulting descriptors, DP-HOT and DP-PB-DCT, are compared with the standard descriptors. Density of a mammogram patch is important for classification, and has not been studied exhaustively. The Image Retrieval in Medical Application (IRMA) database from RWTH Aachen, Germany is a standard database that provides mammogram patches, and most researchers have tested their frameworks only on a subset of patches from this database. We apply our two new descriptors on all images of the IRMA database for density wise classification, and compare with the standard descriptors. We achieve higher accuracy than all of the existing standard descriptors (more than 92%).

cs.CV↗

arXiv2017

Data Backup Network Formation with Heterogeneous Agents

Social storage systems are becoming increasingly popular compared to the existing data backup systems like local, centralized and P2P systems. An endogenously built symmetric social storage model and its aspects like the utility of each agent, bilateral stability, contentment, and efficiency have been extensively discussed in Mane et. al. (2017). We include heterogeneity in this model by using the concept of Social Range Matrix from Kuznetsov et. al (2010). Now, each agent is concerned about its perceived utility, which is a linear combination of its utility as well as others utilities (depending upon whether the pair are friends, enemies or do not care about each other). We derive conditions when two agents may want to add or delete a link, and provide an algorithm that checks if a bilaterally stable network is possible or not. Finally, we take some special Social Range Matrices and prove that under certain conditions on network parameters, a bilaterally stable network is unique.

cs.MA↗

arXiv2017

Stability Analysis of Bilinear Iterative Rational Krylov Algorithm

Models coming from different physical applications are very large in size. Simulation with such systems is expensive so one usually obtains a reduced model (by model reduction) that replicates the input-output behaviour of the original full model. A recently proposed algorithm for model reduction of bilinear dynamical systems, Bilinear Iterative Rational Krylov Algorithm (BIRKA), does so in a locally optimal way. This algorithm requires solving very large linear systems of equations. Usually these systems are solved by direct methods (e.g., LU), which are very expensive. A better choice is iterative methods (e.g., Krylov). However, iterative methods introduce errors in linear solves because they are not exact. They solve the given linear system up to a certain tolerance. We prove that under some mild assumptions BIRKA is stable with respect to the error introduced by the inexact linear solves. We also analyze the accuracy of the reduced system obtained from using these inexact solves and support all our results by numerical experiments.

math.NA↗

arXiv2017

Preconditioned Iterative Solves in Model Reduction of Second Order Linear Dynamical Systems

Recently a new algorithm for model reduction of second order linear dynamical systems with proportional damping, the Adaptive Iterative Rational Global Arnoldi (AIRGA) algorithm, has been proposed. The main computational cost of the AIRGA algorithm is in solving a sequence of linear systems. These linear systems do change only slightly from one iteration step to the next. Here we focus on efficiently solving these systems by iterative methods and the choice of an appropriate preconditioner. We propose the use of relevant iterative algorithm and the Sparse Approximate Inverse (SPAI) preconditioner. A technique to cheaply update the SPAI preconditioner in each iteration step of the model order reduction process is given. Moreover, it is shown that under certain conditions the AIRGA algorithm is stable with respect to the error introduced by iterative methods. Our theory is illustrated by experiments. It is demonstrated that SPAI preconditioned Conjugate Gradient (CG) works well for model reduction of a one dimensional beam model with AIRGA algorithm. Moreover, the computation time of preconditioner with update is on an average 2/3 rd of the computation time of preconditioner without update. With average timings running into hours for very large systems, such savings are substantial.

math.NA↗

arXiv2015

Recycling Krylov subspaces for CFD applications and a new hybrid recycling solver

We focus on robust and efficient iterative solvers for the pressure Poisson equation in incompressible Navier-Stokes problems. Preconditioned Krylov subspace methods are popular for these problems, with BiCGStab and GMRES(m) most frequently used for nonsymmetric systems. BiCGStab is popular because it has cheap iterations, but it may fail for stiff problems, especially early on as the initial guess is far from the solution. Restarted GMRES is better, more robust, in this phase, but restarting may lead to very slow convergence. Therefore, we evaluate the rGCROT method for these systems. This method recycles a selected subspace of the search space (called recycle space) after a restart. This generally improves the convergence drastically compared with GMRES(m). Recycling subspaces is also advantageous for subsequent linear systems, if the matrix changes slowly or is constant. However, rGCROT iterations are still expensive in memory and computation time compared with those of BiCGStab. Hence, we propose a new, hybrid approach that combines the cheap iterations of BiCGStab with the robustness of rGCROT. For the first few time steps the algorithm uses rGCROT and builds an effective recycle space, and then it recycles that space in the rBiCGStab solver. We evaluate rGCROT on a turbulent channel flow problem, and we evaluate both rGCROT and the new, hybrid combination of rGCROT and rBiCGStab on a porous medium flow problem. We see substantial performance gains on both problems.

math.NA↗

arXiv2015

Social Cloud: Concept, Current Trends and Future Scope

In recent years, various kinds of distributed resource sharing setups have been proposed by taking social relationships into consideration. These dissimilar resource sharing setups are tagged as Social Cloud. These setups have appeared in various distributed computing forms such as community cloud, grid, volunteer computing and network services. Such setups are discrete in nature, and hence, do not conceptualize the totality of the Social Cloud concept. In fact, it is difficult to conceptualize Social Cloud without a general framework. There are three main objectives of this work. First, to present a general framework of Social Cloud. Second, to report various Social Cloud setups with corresponding architectural prototypes and current trends. Third, to discuss research challenges.

cs.CY↗

arXiv2015

Recycling BiCGSTAB with an Application to Parametric Model Order Reduction

Krylov subspace recycling is a process for accelerating the convergence of sequences of linear systems. Based on this technique, the recycling BiCG algorithm has been developed recently. Here, we now generalize and extend this recycling theory to BiCGSTAB. Recycling BiCG focuses on efficiently solving sequences of dual linear systems, while the focus here is on efficiently solving sequences of single linear systems (assuming non-symmetric matrices for both recycling BiCG and recycling BiCGSTAB). As compared with other methods for solving sequences of single linear systems with non-symmetric matrices (e.g., recycling variants of GMRES), BiCG based recycling algorithms, like recycling BiCGSTAB, have the advantage that they involve a short-term recurrence, and hence, do not suffer from storage issues and are also cheaper with respect to the orthogonalizations. We modify the BiCGSTAB algorithm to use a recycle space, which is built from left and right approximate invariant subspaces. Using our algorithm for a parametric model order reduction example gives good results. We show about 40% savings in the number of matrix-vector products and about 35% savings in runtime.

math.NA↗

arXiv2011

Recycling BiCG with an Application to Model Reduction

Science and engineering problems frequently require solving a sequence of dual linear systems. Besides having to store only few Lanczos vectors, using the BiConjugate Gradient method (BiCG) to solve dual linear systems has advantages for specific applications. For example, using BiCG to solve the dual linear systems arising in interpolatory model reduction provides a backward error formulation in the model reduction framework. Using BiCG to evaluate bilinear forms -- for example, in quantum Monte Carlo (QMC) methods for electronic structure calculations -- leads to a quadratic error bound. Since our focus is on sequences of dual linear systems, we introduce recycling BiCG, a BiCG method that recycles two Krylov subspaces from one pair of dual linear systems to the next pair. The derivation of recycling BiCG also builds the foundation for developing recycling variants of other bi-Lanczos based methods, such as CGS, BiCGSTAB, QMR, and TFQMR. We develop an augmented bi-Lanczos algorithm and a modified two-term recurrence to include recycling in the iteration. The recycle spaces are approximate left and right invariant subspaces corresponding to the eigenvalues closest to the origin. These recycle spaces are found by solving a small generalized eigenvalue problem alongside the dual linear systems being solved in the sequence. We test our algorithm in two application areas. First, we solve a discretized partial differential equation (PDE) of convection-diffusion type. Such a problem provides well-known test cases that are easy to test and analyze further. Second, we use recycling BiCG in the Iterative Rational Krylov Algorithm (IRKA) for interpolatory model reduction. IRKA requires solving sequences of slowly changing dual linear systems. We show up to 70% savings in iterations, and also demonstrate that for a model reduction problem BiCG takes (about) 50% more time than recycling BiCG.

math.NA↗

arXiv2011

Improved Scaling for Quantum Monte Carlo on Insulators

Quantum Monte Carlo (QMC) methods are often used to calculate properties of many body quantum systems. The main cost of many QMC methods, for example the variational Monte Carlo (VMC) method, is in constructing a sequence of Slater matrices and computing the ratios of determinants for successive Slater matrices. Recent work has improved the scaling of constructing Slater matrices for insulators so that the cost of constructing Slater matrices in these systems is now linear in the number of particles, whereas computing determinant ratios remains cubic in the number of particles. With the long term aim of simulating much larger systems, we improve the scaling of computing the determinant ratios in the VMC method for simulating insulators by using preconditioned iterative solvers. The main contribution of this paper is the development of a method to efficiently compute for the Slater matrices a sequence of preconditioners that make the iterative solver converge rapidly. This involves cheap preconditioner updates, an effective reordering strategy, and a cheap method to monitor instability of ILUTP preconditioners. Using the resulting preconditioned iterative solvers to compute determinant ratios of consecutive Slater matrices reduces the scaling of QMC algorithms from O(n^3) per sweep to roughly O(n^2), where n is the number of particles, and a sweep is a sequence of n steps, each attempting to move a distinct particle. We demonstrate experimentally that we can achieve the improved scaling without increasing statistical errors. Our results show that preconditioned iterative solvers can dramatically reduce the cost of VMC for large(r) systems.

cond-mat.str-el↗