Piotr Berman

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111ranked-venue papers
89as first author
3since 2021 · last 2024
0000-0002-2363-3535ORCID · verified

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Theory of computation · 79 · 73 first-author · 3 since 2021Applied, interdisciplinary, general and emerging computing · 13 · 3 first-authorSystems, architecture and hardware · 10 · 6 first-authorComputer networks · 4 · 2 first-authorGraphics, computer vision, multimedia, augmented reality and games · 3 · 3 first-authorArtificial intelligence and machine learning · 2 · 2 first-authorSecurity and privacy · 1Databases, data management, data science and information retrieval · 1 · 1 first-author
YearPublicationVenuePosition
2024 Testing Connectedness of Images
Piotr Berman, Meiram Murzabulatov, Sofya Raskhodnikova, Dragos Ristache
Algorithmica1
2023 Testing Connectedness of Images
abstract
https://drops.dagstuhl.de/storage/00lipics/lipics-vol275-approx-random2023/LIPIcs.APPROX-RANDOM.2023.66/LIPIcs.APPROX-RANDOM.2023.66.pdf
Piotr Berman, Meiram Murzabulatov, Sofya Raskhodnikova, Dragos Ristache
APPROX/RANDOM1
2022 Tolerant Testers of Image Properties
abstract
We initiate a systematic study of tolerant testers of image properties or, equivalently, algorithms that approximate the distance from a given image to the desired property. Image processing is a particularly compelling area of applications for sublinear-time algorithms and, specifically, property testing. However, for testing algorithms to reach their full potential in image processing, they have to be tolerant, which allows them to be resilient to noise. We design efficient approximation algorithms for the following fundamental questions: What fraction of pixels have to be changed in an image so it becomes a half-plane? A representation of a convex object? A representation of a connected object? More precisely, our algorithms approximate the distance to three basic properties (being a half-plane, convexity, and connectedness) within a small additive error ε, after reading poly (1/ε) pixels, independent of the image size. We also design an efficient agnostic proper PAC learner of convex sets (continuous and discrete) in two dimensions under the uniform distribution. Our algorithms require very simple access to the input: uniform random samples for the half-plane property and convexity, and samples from uniformly random blocks for connectedness. However, the analysis of the algorithms, especially for convexity, requires many geometric and combinatorial insights. For example, in the analysis of the algorithm for convexity, we define a set of reference polygons P ε such that (1) every convex image has a nearby polygon in P ε and (2) one can use dynamic programming to quickly compute the smallest empirical distance to a polygon in P ε .
Piotr Berman, Meiram Murzabulatov, Sofya Raskhodnikova
ACM Trans. Algorithms1
2019 The Power and Limitations of Uniform Samples in Testing Properties of Figures
Piotr Berman, Meiram Murzabulatov, Sofya Raskhodnikova
Algorithmica1
2016 Testing Convexity of Figures Under the Uniform Distribution
abstract
In this paper we present several results on the expected complexity of a convex hull of $n$ points chosen uniformly and independently from a convex shape. (i) We show that the expected number of vertices of the convex hull of $n$ points, chosen uniformly and independently from a disk is $O(n^{1/3})$, and $O(k \log{n})$ for the case a convex polygon with $k$ sides. Those results are well known (see \cite{rs-udkhv-63,r-slcdn-70,ps-cgi-85}), but we believe that the elementary proof given here are simpler and more intuitive. (ii) Let $\D$ be a set of directions in the plane, we define a generalized notion of convexity induced by $\D$, which extends both rectilinear convexity and standard convexity. We prove that the expected complexity of the $\D$-convex hull of a set of $n$ points, chosen uniformly and independently from a disk, is $O(n^{1/3} + \sqrt{nα(\D)})$, where $α(\D)$ is the largest angle between two consecutive vectors in $\D$. This result extends the known bounds for the cases of rectilinear and standard convexity. (iii) Let $\B$ be an axis parallel hypercube in $\Re^d$. We prove that the expected number of points on the boundary of the quadrant hull of a set $S$ of $n$ points, chosen uniformly and independently from $\B$ is $O(\log^{d-1}n)$. Quadrant hull of a set of points is an extension of rectilinear convexity to higher dimensions. In particular, this number is larger than the number of maxima in $S$, and is also larger than the number of points of $S$ that are vertices of the convex hull of $S$. Those bounds are known \cite{bkst-anmsv-78}, but we believe the new proof is simpler.
Piotr Berman, Meiram Murzabulatov, Sofya Raskhodnikova
SoCG1
2016 The Power and Limitations of Uniform Samples in Testing Properties of Figures
abstract
We investigate testing of properties of 2-dimensional figures that consist of a black object on a white background. Given a parameter epsilon in (0,1/2), a tester for a specified property has to accept with probability at least 2/3 if the input figure satisfies the property and reject with probability at least 2/3 if it does not. In general, property testers can query the color of any point in the input figure. We study the power of testers that get access only to uniform samples from the input figure. We show that for the property of being a half-plane, the uniform testers are as powerful as general testers: they require only O(1/epsilon) samples. In contrast, we prove that convexity can be tested with O(1/epsilon) queries by testers that can make queries of their choice while uniform testers for this property require Omega(1/epsilon^{5/4}) samples. Previously, the fastest known tester for convexity needed Theta(1/epsilon^{4/3}) queries.
Piotr Berman, Meiram Murzabulatov, Sofya Raskhodnikova
FSTTCS1
2016 Tolerant Testers of Image Properties
Piotr Berman, Meiram Murzabulatov, Sofya Raskhodnikova
ICALP1
2014 Lp-testing
abstract
We initiate a systematic study of sublinear algorithms for approximately testing properties of real-valued data with respect to Lp distances for p = 1, 2. Such algorithms distinguish datasets which either have (or are close to having) a certain property from datasets which are far from having it with respect to Lp distance. For applications involving noisy real-valued data, using Lp distances allows algorithms to withstand noise of bounded Lp norm. While the classical property testing framework developed with respect to Hamming distance has been studied extensively, testing with respect to Lp distances has received little attention.
Piotr Berman, Sofya Raskhodnikova, Grigory Yaroslavtsev
STOC1
2014 On the Computational Complexity of Measuring Global Stability of Banking Networks
Piotr Berman, Bhaskar DasGupta, Lakshmi Kaligounder, Marek Karpinski
Algorithmica1
2014 Approximation Algorithms for Min-Max Generalization Problems
abstract
We provide improved approximation algorithms for the min-max generalization problems considered by Du, Eppstein, Goodrich, and Lueker [Du et al. 2009]. Generalization is widely used in privacy-preserving data mining and can also be viewed as a natural way of compressing a dataset. In min-max generalization problems, the input consists of data items with weights and a lower bound w lb , and the goal is to partition individual items into groups of weight at least w lb while minimizing the maximum weight of a group. The rules of legal partitioning are specific to a problem. Du et al. consider several problems in this vein: (1) partitioning a graph into connected subgraphs, (2) partitioning unstructured data into arbitrary classes, and (3) partitioning a two-dimensional array into contiguous rectangles (subarrays) that satisfy these weight requirements. We significantly improve approximation ratios for all the problems considered by Du et al. and provide additional motivation for these problems. Moreover, for the first problem, whereas Du et al. give approximation algorithms for specific graph families, namely, 3-connected and 4-connected planar graphs, no approximation algorithm that works for all graphs was known prior to this work.
Piotr Berman, Sofya Raskhodnikova
ACM Trans. Algorithms1
2014 HybridPlan: a capacity planning technique for projecting storage requirements in hybrid storage systems
Youngjae Kim 0001, Bhuvan Urgaonkar, Piotr Berman, Anand Sivasubramaniam
J. Supercomput.4
2013 Approximation algorithms for spanner problems and Directed Steiner Forest
Piotr Berman, Arnab Bhattacharyya 0001, Konstantin Makarychev, Sofya Raskhodnikova, Grigory Yaroslavtsev
Inf. Comput.1
2012 Primal-Dual Approximation Algorithms for Node-Weighted Network Design in Planar Graphs
Piotr Berman, Grigory Yaroslavtsev
APPROX-RANDOM1
2012 Exact and Approximation Algorithms for Geometric and Capacitated Set Cover Problems
Piotr Berman, Marek Karpinski, Andrzej Lingas
Algorithmica1
2011 O(1)-Approximations for Maximum Movement Problems
Piotr Berman, Erik D. Demaine, Morteza Zadimoghaddam
APPROX-RANDOM1
2011 Steiner Transitive-Closure Spanners of Low-Dimensional Posets
Piotr Berman, Arnab Bhattacharyya 0001, Elena Grigorescu, Sofya Raskhodnikova, David P. Woodruff, Grigory Yaroslavtsev
ICALP (1)1
2011 Improved Approximation for the Directed Spanner Problem
Piotr Berman, Arnab Bhattacharyya 0001, Konstantin Makarychev, Sofya Raskhodnikova, Grigory Yaroslavtsev
ICALP (1)1
2011 HybridStore: A Cost-Efficient, High-Performance Storage System Combining SSDs and HDDs
abstract
Unlike the use of DRAM for caching or buffering, certain idiosyncrasies of SSDs make their integration into existing systems non-trivial. Flash memory suffers from limits on its reliability, is an order of magnitude more expensive than the HDD, and can sometimes be as slow as the HDD (due to excessive garbage collection (GC) induced by high intensity of random writes). Given these trade-offs between HDDs and SSDs in terms of cost, performance, and lifetime, the current consensus among several storage experts is to view SSDs not as a replacement for HDD but rather as a complementary device within the high performance storage hierarchy. We design and evaluate such a hybrid system called Hybrid Store to provide: (a) Hybrid Plan: improved capacity planning technique to administrators with the overall goal of operating within cost-budgets and (b) HybridDyn: improved performance/lifetime guarantees during episodes of deviations from expected workloads through two novel mechanisms: write-regulation and fragmentation busting. As an illustrative example of HybridStore's efficacy, Hybrid Plan is able to find the most cost-effective storage configuration for a large scale workload of Microsoft Research and suggest one MLC SSD with ten 7.2K RPM HDDs instead of fourteen 7.2K RPM HDDs only. HybridDyn is able to reduce the average response time for an enterprise scale random-write dominant workload by about 71%as compared to a HDD-based system.
Youngjae Kim 0001, Bhuvan Urgaonkar, Piotr Berman, Anand Sivasubramaniam
MASCOTS4
2011 Optimizing sensor movement planning for energy efficiency
abstract
Conserving the energy for motion is an important yet not-well-addressed problem in mobile sensor networks. In this article, we study the problem of optimizing sensor movement for energy efficiency. We adopt a complete energy model to characterize the entire energy consumption in movement. Based on the model, we propose an optimal trapezoidal velocity schedule for minimizing energy consumption when the road condition is uniform; and a corresponding velocity schedule for the variable road condition by using continuous-state dynamic programming. Considering the variety in motion hardware, we also design one velocity schedule for simple microcontrollers, and one velocity schedule for relatively complex microcontrollers, respectively. Simulation results show that our velocity planning may have significant impact on energy conservation.
Grace Guiling Wang, Mary Jane Irwin, Haoying Fu, Piotr Berman, Wensheng Zhang 0001, Thomas La Porta
ACM Trans. Sens. Networks4
2010 Approximation Algorithms for Min-Max Generalization Problems
Piotr Berman, Sofya Raskhodnikova
APPROX-RANDOM1
2010 Exact and Approximation Algorithms for Geometric and Capacitated Set Cover Problems
Piotr Berman, Marek Karpinski, Andrzej Lingas
COCOON1
2010 Finding Sparser Directed Spanners
abstract
A spanner of a graph is a sparse subgraph that approximately preserves distances in the original graph. More precisely, a subgraph $H = (V,E_H)$ is a $k$-spanner of a graph $G=(V,E)$ if for every pair of vertices $u,v \in V$, the shortest path distance $dist_H(u,v)$ from $u$ to $v$ in $H$ is at most $k.dist_G(u,v)$. We focus on spanners of directed graphs and a related notion of transitive-closure spanners. The latter captures the idea that a spanner should have a small diameter but preserve the connectivity of the original graph. We study the computational problem of finding the sparsest $k$-spanner (resp., $k$-TC-spanner) of a given directed graph, which we refer to as DIRECTED $k$-SPANNER (resp., $k$-TC-SPANNER). We improve all known approximation algorithms for these problems for $k\geq 3$. (For $k=2$, the current ratios are tight, assuming P$\neq$NP.) Along the way, we prove several structural results about the size of the sparsest spanners of directed graphs.
Piotr Berman, Sofya Raskhodnikova, Ge Ruan
FSTTCS1
2010 A 3/2-Approximation Algorithm for Generalized Steiner Trees in Complete Graphs with Edge Lengths 1 and 2
Piotr Berman, Marek Karpinski, Alex Zelikovsky
ISAAC (1)1
2010 Successes and Failures of Elegant Algorithms in Computational Biology
Piotr Berman
ISBRA1
2009 Approximating Transitive Reductions for Directed Networks
Piotr Berman, Bhaskar DasGupta, Marek Karpinski
WADS1
2009 1.25-Approximation Algorithm for Steiner Tree Problem with Distances 1 and 2
Piotr Berman, Marek Karpinski, Alex Zelikovsky
WADS1
2009 Consistent Sets of Secondary Structures in Proteins
Piotr Berman, Jieun K. Jeong
Algorithmica1
2009 On approximating four covering and packing problems
Mary V. Ashley, Tanya Y. Berger-Wolf, Piotr Berman, W. Art Chaovalitwongse, Bhaskar DasGupta, Ming-Yang Kao
J. Comput. Syst. Sci.3
2008 Fast Alignments of Metabolic Networks
abstract
Network alignments are extensively used for comparing, exploring, and predicting biological networks. Existing alignment tools are mostly based on isomorphic and homeomorphic embedding and require solving a problem that is NP-complete even when searching a match for a tree in acyclic networks. On the other hand, if the mapping of different nodes from the query network (pattern) into the same node from the text network is allowed, then trees can be optimally mapped into arbitrary networks in polynomial time.In this paper we present the first polynomial-time algorithm for finding the best matching pair consisting of a subtree in a given tree pattern and a subgraph in a given text (represented by an arbitrary network) when both insertions and deletions of degree-2 vertices are allowed on any path. Our dynamic programming algorithm is an order of magnitude faster than the previous network alignment algorithm when deletions are forbidden. The algorithm has been also generalized to pattern networks with cycles: with a modest increase in runtime it can handle patterns with the limited vertex feedback set.We have applied our algorithm to matching metabolic pathways of four organisms (E. coli, S. cerevisiae, B. subtilis and T. thermophilus species) and found a reasonably large set of statistically significant alignments. We show advantages of allowing pattern vertex deletions and give an example validating biological relevance of the pathway alignment.
Qiong Cheng, Piotr Berman, Robert W. Harrison, Alex Zelikovsky
BIBM2
2008 HCV Quasispecies Assembly Using Network Flows
Kelly Westbrooks, Irina Astrovskaya, David S. Campo, Yuri Khudyakov, Piotr Berman, Alex Zelikovsky
ISBRA5
2008 Improving Strand Pairing Prediction through Exploring Folding Cooperativity
abstract
The topology of beta-sheets is defined by the pattern of hydrogen-bonded strand pairing. Therefore, predicting hydrogen bonded strand partners is a fundamental step towards predicting beta-sheet topology. At the same time, finding the correct partners is very difficult due to long range interactions involved in strand pairing. Additionally, patterns of amino acids involved, in beta-sheet formations are very general and therefore difficult to use for computational recognition of specific contacts between strands. In this work, we report a new strand pairing algorithm. To address above mentioned difficulties, our algorithm attempts to mimic elements of the folding process. Namely, in addition to ensuring that the predicted hydrogen bonded strand pairs satisfy basic global consistency constraints, it takes into account hypothetical folding pathways. Consistently with this view, introducing hydrogen bonds between a pair of strands changes the probabilities of forming hydrogen bonds between other pairs of strand. We demonstrate that this approach provides an improvement over previously proposed algorithms. We also compare the performance of this method to that of a global optimization algorithm that poses the problem as integer linear programming optimization problem and solves it using ILOG CPLEX package.
Jieun K. Jeong, Piotr Berman, Teresa M. Przytycka
IEEE ACM Trans. Comput. Biol. Bioinform.2
2008 Approximating the online set multicover problems via randomized winnowing
Piotr Berman, Bhaskar DasGupta
Theor. Comput. Sci.1
2007 Packing to angles and sectors
abstract
Motivated by the widespread proliferation of wireless networks employing directional antennas, we study some capacitated covering problems arising in these networks. Geometrically, the area covered by a directional antenna with parameters α,ρ,r is a set of points with polar coordinates (r,θ) such that r ≤ r and α ≤ θ ≤ α + ρ. Given a set of customers, their positions on the plane and their bandwidth demands, the capacitated covering problem considered here is to cover all the customers with the minimum number of directional antennas such that the demands of customers assigned to an antenna stays within a bound. We consider two settings of this capacitated cover problem arising in wireless networks. In the first setting where the antennas have variable angular range, we present an approximation algorithm with ratio 3. In the setting where the angular range of antennas is fixed, we improve this approximation ratio to 1.5.
Piotr Berman, Jieun K. Jeong, Shiva Prasad Kasiviswanathan, Bhuvan Urgaonkar
SPAA1
2007 Bringing Folding Pathways into Strand Pairing Prediction
Jieun K. Jeong, Piotr Berman, Teresa M. Przytycka
WABI2
2007 Faster Approximation of Distances in Graphs
Piotr Berman, Shiva Prasad Kasiviswanathan
WADS1
2007 Foreword
Piotr Berman, Bhaskar DasGupta, Jie Liang 0002
Algorithmica1
2007 HomologMiner: looking for homologous genomic groups in whole genomes
abstract
MOTIVATION: Complex genomes contain numerous repeated sequences, and genomic duplication is believed to be a main evolutionary mechanism to obtain new functions. Several tools are available for de novo repeat sequence identification, and many approaches exist for clustering homologous protein sequences. We present an efficient new approach to identify and cluster homologous DNA sequences with high accuracy at the level of whole genomes, excluding low-complexity repeats, tandem repeats and annotated interspersed repeats. We also determine the boundaries of each group member so that it closely represents a biological unit, e.g. a complete gene, or a partial gene coding a protein domain. RESULTS: We developed a program called HomologMiner to identify homologous groups applicable to genome sequences that have been properly marked for low-complexity repeats and annotated interspersed repeats. We applied it to the whole genomes of human (hg17), macaque (rheMac2) and mouse (mm8). Groups obtained include gene families (e.g. olfactory receptor gene family, zinc finger families), unannotated interspersed repeats and additional homologous groups that resulted from recent segmental duplications. Our program incorporates several new methods: a new abstract definition of consistent duplicate units, a new criterion to remove moderately frequent tandem repeats, and new algorithmic techniques. We also provide preliminary analysis of the output on the three genomes mentioned above, and show several applications including identifying boundaries of tandem gene clusters and novel interspersed repeat families. AVAILABILITY: All programs and datasets are downloadable from www.bx.psu.edu/miller_lab.
Minmei Hou, Piotr Berman, Chih-Hao Hsu, Robert S. Harris
Bioinform.2
2007 The inverse protein folding problem on 2D and 3D lattices
Piotr Berman, Bhaskar DasGupta, Dhruv Mubayi, Robert H. Sloan, György Turán, Yi Zhang 0002
Discret. Appl. Math.1
2007 Randomized approximation algorithms for set multicover problems with applications to reverse engineering of protein and gene networks
Piotr Berman, Bhaskar DasGupta, Eduardo D. Sontag
Discret. Appl. Math.1
2007 Computational complexity of some restricted instances of 3-SAT
Piotr Berman, Marek Karpinski, Alex D. Scott
Discret. Appl. Math.1
2007 On constructing an optimal consensus clustering from multiple clusterings
Piotr Berman, Bhaskar DasGupta, Ming-Yang Kao, Jie Wang 0002
Inf. Process. Lett.1
2007 Optimal trade-off for Merkle tree traversal
Piotr Berman, Marek Karpinski, Yakov Nekrich
Theor. Comput. Sci.1
2007 Bidding Protocols for Deploying Mobile Sensors
abstract
Constructing a sensor network with a mix of mobile and static sensors can achieve a balance between sensor coverage and sensor cost. In this paper, we design two bidding protocols to guide the movement of mobile sensors in such sensor networks to increase the coverage to a desirable level. In the protocols, static sensors detect coverage holes locally by using Voronoi diagrams and bid mobile sensors to move. Mobile sensors accept the highest bids and heal the largest holes. Simulation results show that our protocols achieve suitable trade-off between coverage and sensor cost
Grace Guiling Wang, Guohong Cao, Piotr Berman, Thomas La Porta
IEEE Trans. Mob. Comput.3
2006 8/7-approximation algorithm for (1, 2)-TSP
Piotr Berman, Marek Karpinski
SODA1
2006 Controlling Size When Aligning Multiple Genomic Sequences with Duplications
Minmei Hou, Piotr Berman, Louxin Zhang, Webb Miller
WABI2
2006 A Linear-Time Algorithm for Studying Genetic Variation
Nikola Stojanovic, Piotr Berman
WABI2
2005 Optimizing sensor movement planning for energy efficiency
abstract
Conserving the energy for motion is an important yet not-well-addressed problem in mobile sensor networks. In this paper, we study the problem of optimizing sensor movement for energy efficiency. We adopt a complete energy model to characterize the entire energy consumption in movement. Based on the model, we propose an optimal velocity schedule for minimizing energy consumption when the road condition is uniform; and a near optimal velocity schedule for the variable road condition by using continuous-state dynamic programming. Considering the variety in motion hardware, we also design one velocity schedule for simple microcontrollers, and one velocity schedule for relatively complex microcontrollers, respectively. Simulation results show that our velocity planning may have significant impact on energy conservation
Grace Guiling Wang, Mary Jane Irwin, Piotr Berman, Haoying Fu, Thomas La Porta
ISLPED3
2005 Approximating the Online Set Multicover Problems via Randomized Winnowing
Piotr Berman, Bhaskar DasGupta
WADS1
2005 On the Vehicle Routing Problem
Piotr Berman, Surajit K. Das
WADS1
2005 Tight approximability results for test set problems in bioinformatics
Piotr Berman, Bhaskar DasGupta, Ming-Yang Kao
J. Comput. Syst. Sci.1
2004 Randomized Approximation Algorithms for Set Multicover Problems with Applications to Reverse Engineering of Protein and Gene Networks
Piotr Berman, Bhaskar DasGupta, Eduardo D. Sontag
APPROX-RANDOM1
2004 The Protein Sequence Design Problem in Canonical Model on 2D and 3D Lattices
Piotr Berman, Bhaskar DasGupta, Dhruv Mubayi, Robert H. Sloan, György Turán, Yi Zhang 0002
CPM1
2004 Power efficient monitoring management in sensor networks
abstract
Optimizing the energy consumption in wireless sensor networks has recently become the most important performance objective. We assume the sensor network model in which sensors can interchange idle and active modes. Given monitoring regions, battery life and energy consumption rate for each sensor, we formulate the problem of maximizing sensor network lifetime, i.e., time during which the monitored area is (partially or fully) covered. Our contributions include (1) an efficient data structure to represent the monitored area with at most n/sup 2/ points guaranteeing the full coverage which is superior to the previously used approach based on grid points, (2) efficient provably good centralized algorithms for sensor monitoring schedule maximizing the total lifetime including (1+ln(1-q)/sup -1/)-approximation algorithm for the case when a q-portion of the monitored area is required to cover, e.g., for the 90% area coverage our schedule guarantees to be at most 3.3 times shorter than the optimum, (4) a family of efficient distributed protocols with trade-off between communication and monitoring power consumption, (5) extensive experimental study of the proposed algorithms showing significant advantage in quality, scalability and flexibility.
Piotr Berman, Gruia Calinescu, C. Shah, Alex Zelikovsky
WCNC1
2003 Optimizing misdirection
Piotr Berman, Piotr Krysta
SODA1
2003 Aligning two fragmented sequences
Vamsi Veeramachaneni, Piotr Berman, Webb Miller
Discret. Appl. Math.2
2002 1.375-Approximation Algorithm for Sorting by Reversals
Piotr Berman, Sridhar Hannenhalli, Marek Karpinski
ESA1
2002 Approximation Hardness of Bounded Degree MIN-CSP and MIN-BISECTION
Piotr Berman, Marek Karpinski
ICALP1
2002 Approximating Huffman Codes in Parallel
Piotr Berman, Marek Karpinski, Yakov Nekrich
ICALP1
2002 Slice and dice: a simple, improved approximate tiling recipe
Piotr Berman, Bhaskar DasGupta, S. Muthukrishnan 0001
SODA1
2002 Simple approximation algorithm for nonoverlapping local alignments
Piotr Berman, Bhaskar DasGupta, S. Muthukrishnan 0001
SODA1
2002 Approximating minimum unsatisfiability of linear equations
Piotr Berman, Marek Karpinski
SODA1
2002 Fast Optimal Genome Tiling with Applications to Microarray Design and Homology Search
Piotr Berman, Paul Bertone, Bhaskar DasGupta, Mark Gerstein, Ming-Yang Kao, Michael Snyder 0001
WABI1
2002 On the Complexity of Pattern Matching for Highly Compressed Two-Dimensional Texts
Piotr Berman, Marek Karpinski, Lawrence L. Larmore, Wojciech Plandowski, Wojciech Rytter
J. Comput. Syst. Sci.1
2002 Exact Size of Binary Space Partitionings and Improved Rectangle Tiling Algorithms
abstract
We prove the following upper and lower bounds on the exact size of binary space partition (BSP) trees for a set of n isothetic rectangles in the plane: An upper bound of 3n-1 in general, and an upper bound of 2n-1 if the rectangles tile the underlying space. This improves the upper bounds of 4n in [V. Hai Nguyen and P. Widmayer, Binary Space Partitions for Sets of Hyperrectangles, Lecture Notes in Comput. Sci. 1023, Springer-Verlag, Berlin, 1995; F. d'Amore and P. G. Franciosa, Inform. Process. Lett., 44 (1992), pp. 255--259]. A BSP satisfying the upper bounds can be constructed in O(n log n) time. A worst-case lower bound of 2n-o(n) in general, and $\frac{3n}{2}-o(n)$ if the rectangles form a tiling. The BSP tree is one of the most popular data structures in computational geometry, and hence even "small" factor improvements of $\frac{4}{3}$ or 2 on the previously known upper bounds that we show improve the performances of applications relying on the BSP tree. As an illustration, we present improved approximation algorithms for certain dual rectangle tiling problems using our upper bounds on the size of the BSP trees.
Piotr Berman, Bhaskar DasGupta, S. Muthukrishnan 0001
SIAM J. Discret. Math.1
2001 Improved approximation algorithms for rectangle tiling and packing
Piotr Berman, Bhaskar DasGupta, S. Muthukrishnan 0001, Suneeta Ramaswami
SODA1
2000 Improvements in throughout maximization for real-time scheduling
abstract
We consider the problem of off-line throughput maximization for job scheduling on one or more machines, where each job has a release time, a deadline and a profit. Most of the versions of the problem discussed here were already treated by Bar-Noy et al.(Proc. 31st ACM STOC, 622-631, 1999). Our main contribution is to provide algorithms that do not use linear programming, are simple and much faster than the corresponding ones proposed in Bar-Noy et al., while either having the same quality of approximation or improving it. More precisely, compared to the results of in Bar-Noy et al., our pseudo-polynomial algorithm for multiple unrelated machines and all of our strongly-polynomial algorithms have better performance ratios, all of our algorithms run much faster, are combinatorial in nature and avoid linear programming. Finally, we show that algorithms with better performance ratios than 2 are possible if the stretch factors of the jobs are bounded.
Piotr Berman, Bhaskar DasGupta
STOC1
2000 Optimal phase conflict removal for layout of dark field alternatingphase shifting masks
abstract
We describe new, efficient algorithms for layout modification and phase assignment for dark field alternating-type phase shifting masks in the single exposure regime. We make the following contributions. First, we suggest new two-coloring and compaction approach that simultaneously optimizes layout and phase assignment which is based on planar embedding of an associated conflict graph. We also describe additional approaches to cooptimization of layout and phase assignment for alternating PSM. Second, we give optimal and fast algorithms to minimize the number of phase conflicts that must be removed to ensure two colorability of the conflict graph. We reduce this problem to the T-join problem which asks for a minimum weight edge set A such that a node u is incident to an odd number of edges of A if u belongs to a given node subset T of a weighted graph. Third, we suggest several practical algorithms for the T-join problem. In sparse graphs, our algorithms are faster than previously known methods. Computational experience with industrial VLSI layout benchmarks shows the advantages of the new algorithms.
Piotr Berman, Andrew B. Kahng, Devendra Vidhani, Alex Zelikovsky
IEEE Trans. Comput. Aided Des. Integr. Circuits Syst.1
1999 On Some Tighter Inapproximability Results (Extended Abstract)
Piotr Berman, Marek Karpinski
ICALP1
1999 Optimal phase conflict removal for layout of dark field alternating phase shifting masks
abstract
We describe new, efficient algorithms for layout modification and phase assignment for dark field alternating-type phase shifting masks in the single exposure regime. We make the following contributions. First, we suggest new two-coloring and compaction approach that simultaneously optimizes layout and phase assignment which is based on planar embedding of an associated conflict graph. We also describe additional approaches to cooptimization of layout and phase assignment for alternating PSM. Second, we give optimal and fast algorithms to minimize the number of phase conflicts that must be removed to ensure two colorability of the conflict graph. We reduce this problem to the -join problem which asks for a minimum weight edge set such that a node is incident to an odd number of edges of if belongs to a given node subset of a weighted graph. Third, we suggest several practical algorithms for the -join problem. In sparse graphs, our algorithms are faster than previously known methods. Computational experience with industrial VLSI layout benchmarks shows the advantages of the new algorithms.
Piotr Berman, Andrew B. Kahng, Devendra Vidhani, Alex Zelikovsky
ISPD1
1999 Winnowing sequences from a database search
abstract
In database searches for sequence similarity, matches to a distinct sequence region (e.g. protein domain) are frequently obscured by numerous matches to another region of the same sequence.In order to cope with this problem, algorithms are developed to discard redundant matches.One model for this problem begins with a list of intervals, each with an associated score; each interval gives the range of positions in the query sequence that align to a database sequence, and the score is that of the alignment.If interval I is contained in interval J, and I's score is less than J's, then I is said to be dominated by J.The problem is then to identify each interval that is dominated by at least K other intervals, where K is a given level of "tolerable redundancy."An algorithm is developed to solve the problem in O(N log N) time and O(N*) space, where N is the number of intervals and N' is a precisely defined value that never exceeds N and is frequently much smaller.This criterion for discarding database hits has been implemented in the Blast program, as illustrated herein with examples.Several variations and extensions of this approach are also described.
Piotr Berman, Zheng Zhang 0004, Yuri I. Wolf, Eugene V. Koonin, Webb Miller
RECOMB1
1999 The T-join Problem in Sparse Graphs: Applications to Phase Assignment Problem in VLSI Mask Layout
Piotr Berman, Andrew B. Kahng, Devendra Vidhani, Alex Zelikovsky
WADS1
1999 Post-processing long pairwise alignments
abstract
MOTIVATION: The local alignment problem for two sequences requires determining similar regions, one from each sequence, and aligning those regions. For alignments computed by dynamic programming, current approaches for selecting similar regions may have potential flaws. For instance, the criterion of Smith and Waterman can lead to inclusion of an arbitrarily poor internal segment. Other approaches can generate an alignment scoring less than some of its internal segments. RESULTS: We develop an algorithm that decomposes a long alignment into sub-alignments that avoid these potential imperfections. Our algorithm runs in time proportional to the original alignment's length. Practical applications to alignments of genomic DNA sequences are described.
Zheng Zhang 0004, Piotr Berman, Thomas Wiehe, Webb Miller
Bioinform.2
1999 On Approximation Properties of the Independent Set Problem for Low Degree Graphs
Piotr Berman, Toshihiro Fujito
Theory Comput. Syst.1
1999 A 2-Approximation Algorithm for the Undirected Feedback Vertex Set Problem
abstract
A feedback vertex set of a graph is a subset of vertices that contains at least one vertex from every cycle in the graph. The problem considered is that of finding a minimum feedback vertex set given a weighted and undirected graph. We present a simple and efficient approximation algorithm with performance ratio of at most 2, improving previous best bounds for either weighted or unweighted cases of the problem. Any further improvement on this bound, matching the best constant factor known for the vertex cover problem, is deemed challenging. The approximation principle, underlying the algorithm, is based on a generalized form of the classical local ratio theorem, originally developed for approximation of the vertex cover problem, and a more flexible style of its application.
Vineet Bafna, Piotr Berman, Toshihiro Fujito
SIAM J. Discret. Math.2
1998 Adaptability and the Usefulness of Hints (Extended Abstract)
Piotr Berman, Juan A. Garay 0001
ESA1
1998 Alignments without low-scoring regions
abstract
Given a strong match be%een regions of txvo sequences, horn far can the match be meaningfully extended if gaps are all04 in the resdtinrc aknment?The aim is to aviod sear&ix bwond the point th\t asuseful extension of the a&mm& is l&ly to be found.Without loss of generality, we can restrict attention to the suffixes of the sequences that follow the strong match, which leads to the following formal problem.Given two sequences and a fixed X > 0, align initial portions of the sequences subject to the constraint that no section of the alignment scores below -X.Our results indicate that computing an optimal alignment under this constraint is very expensive.However, less rigorous conditions on the alignment can be guaranked by quite eiiicient algorithms.One of these variants has been implemented in a new release of the Blast suite of database search programs.a b C Figure 1: Graph model of a simple alignment problem.Dark edges (corresponding to aligning identical letters) score 1, and all other edges score -1.
Zheng Zhang 0004, Piotr Berman, Webb Miller
RECOMB2
1997 On the Complexity of Pattern Matching for Highly Compressed Two-Dimensional Texts
Piotr Berman, Marek Karpinski, Lawrence L. Larmore, Wojciech Plandowski, Wojciech Rytter
CPM1
1997 Competing against Specialists
Piotr Berman, Juan A. Garay 0001
PODC1
1997 On-Line Algorithms for Steiner Tree Problems (Extended Abstract)
abstract
Article On-line algorithms for Steiner tree problems (extended abstract) Share on Authors: Piotr Berman Penn State University, University Park, PA Penn State University, University Park, PAView Profile , Chris Coulston Penn State University, University Park, PA Penn State University, University Park, PAView Profile Authors Info & Claims STOC '97: Proceedings of the twenty-ninth annual ACM symposium on Theory of computingMay 1997 Pages 344–353https://doi.org/10.1145/258533.258618Published:04 May 1997 56citation1,035DownloadsMetricsTotal Citations56Total Downloads1,035Last 12 Months33Last 6 weeks5 Get Citation AlertsNew Citation Alert added!This alert has been successfully added and will be sent to:You will be notified whenever a record that you have chosen has been cited.To manage your alert preferences, click on the button below.Manage my AlertsNew Citation Alert!Please log in to your account Save to BinderSave to BinderCreate a New BinderNameCancelCreateExport CitationPublisher SiteGet Access
Piotr Berman, Chris Coulston
STOC1
1997 On-line Load Balancing for Related Machines
Piotr Berman, Moses Charikar, Marek Karpinski
WADS1
1997 A Linear-Time Algorithm for the 1-Mismatch Problem
Nikola Stojanovic, Piotr Berman, Deborah Gumucio, Ross C. Hardison, Webb Miller
WADS2
1997 Complexities of Efficient Solutions of Rectilinear Polygon Cover Problems
Piotr Berman, Bhaskar DasGupta
Algorithmica1
1997 A Nearly Optimal Parallel Algorithm for the Voronoi Diagram of a Convex Polygon
Piotr Berman, Andrzej Lingas
Theor. Comput. Sci.1
1996 Fast Sorting by Reversal
Piotr Berman, Sridhar Hannenhalli
CPM1
1996 Randomized Robot Navigation Algorithms
Piotr Berman, Avrim Blum, Amos Fiat, Howard J. Karloff, Adi Rosén, Michael E. Saks
SODA1
1995 Constant Ratio Approximations of the Weighted Feedback Vertex Set Problem for Undirected Graphs
Vineet Bafna, Piotr Berman, Toshihiro Fujito
ISAAC2
1995 On the Approximation Properties of Independent Set Problem in Degree 3 Graphs
Piotr Berman, Toshihiro Fujito
WADS1
1994 Approaching the 5/4-Approximation for Rectilinear Steiner Trees
Piotr Berman, Ulrich Fößmeier, Marek Karpinski, Michael Kaufmann 0001, Alex Zelikovsky
ESA1
1994 Approximating Maximum Independent Set in Bounded Degree Graphs
Piotr Berman, Martin Fürer
SODA1
1994 Reliable distributed diagnosis for multiprocessor systems with random faults
abstract
Abstract We study a probabilistic setting for distributed fault diagnosis in multiprocessor systems. A system is an undirected graph with nodes representing processors and edges representing communication links. Processors are assumed to fail independently with some probability p. They test their neighbors, and a fault‐free processor has probability 1 − q of discovering a fault of a failed neighbor in an individual test. Subsequently, fault‐free processors attempt to diagnose all the processors of the system with communication based on the test results. During communication, the behavior of faulty processors may be arbitrary (socalled malicious). For every p ≤ ½, q ≤ 1, we construct systems with O(n log n) links in which distributed probabilistic diagnosis can be achieved with probability of correctness at least 1 − n−1. We also show that for some small fixed p and q a similar result holds for the hypercube. On the other hand, we prove that for sufficiently small k, for a system with n processors and kn log n links, the probability of achieving correct diagnosis cannot exceed n−0.5. © 1994 by John Wiley & Sons, Inc.
Piotr Berman, Andrzej Pelc
Networks1
1994 Voting as the Optimal Static Pessimistic Scheme for Managing Replicated Data
abstract
This paper investigates the problem of finding an optimal static pessimistic replica control scheme. It has been widely accepted that coteries (proposed by Garcia-Molina and Barbara) provide the most general framework for such schemes. We demonstrate that voting schemes, a very small subset of static pessimistic schemes, are optimal for fully connected networks with negligible link failure rates, as well as for Ethernet systems. We also show that voting is not optimal for somewhat more general systems. We propose a modification of the algorithm of Z. Tong and R.Y. Kain (1988) for computing optimal voting in operation independent case, so that it runs in linear (rather than exponential) time. Finally, we propose the first efficient algorithm for computing the optimal vote assignment and appropriate thresholds for fully connected networks when relative frequencies of read and write operations are known. We also extend this result to Ethernet systems.>
Mirjana Spasojevic, Piotr Berman
IEEE Trans. Parallel Distributed Syst.2
1993 Fast Consensus in Networks of Bounded Degree
Piotr Berman, Juan A. Garay 0001
Distributed Comput.1
1993 Cloture Votes: n/4-Resilient Distributed Consensus in t+1 Rounds
Piotr Berman, Juan A. Garay 0001
Math. Syst. Theory1
1992 On-Line Navigation in a Room
Eldad Bar-Eli, Piotr Berman, Amos Fiat, Peiyuan Yan
SODA2
1992 Improved Approximations for the Steiner Tree Problem
Piotr Berman, Viswanathan Ramaiyer
SODA1
1992 On the Complexity of Approximating the Independent Set Problem
Piotr Berman, Georg Schnitger
Inf. Comput.1
1992 A note on the complexity of reliability in neural networks
abstract
It is shown that in a standard discrete neural network model with small fan-in, tolerance to random malicious faults can be achieved with a log-linear increase in the number of neurons and a constant factor increase in parallel time, provided fan-in can increase arbitrarily. A similar result is obtained for a nonstandard but closely related model with no restriction on fan-in.
Piotr Berman, Ian Parberry, Georg Schnitger
IEEE Trans. Neural Networks1
1990 A Competitive 3-Server Algorithm
Piotr Berman, Howard J. Karloff, Gábor Tardos
SODA1
1990 Voting as the Optimal Static Pessimistic Scheme for Managing Replicated Data
abstract
The problem of finding an optimal static pessimistic replica control scheme is investigated. It has been widely accepted that coteries (proposed by Garcia-Molina and Barbara) provide the most general framework for such schemes. Under such as assumption, it is demonstrated that the voting scheme is an optimal static pessimistic scheme for fully connected networks with negligible link failure rates, as well as for Ethernet systems. It is also shown that voting is not optimal for somewhat more general systems. The authors propose a modification of the algorithm of Tong and Kain for the best voting in the operation-independent case so that it runs in linear (rather than exponential) time. They also propose a linear-time algorithm for computing the optimal vote assignment when relative frequencies of read and write operations are known.>
Mirjana Obradovic, Piotr Berman
SRDS2
1989 Towards Optimal Distributed Consensus (Extended Abstract)
abstract
In a distributed consensus protocol all processors (of which t may be faulty) are given (binary) initial values; after exchanging messages all correct processors must agree on one of them. The quality of a protocol is measured here using as parameters the total number of processors n, number of rounds of message exchange r, and maximal message length m, with optima, respectively, of 3t+1, t+1, and 1. Although no known protocol is optimal in all these three aspects simultaneously, the protocols that take further steps in this direction are presented. The first protocol has n>4t, r=t+1, and polynomial message size. The second protocol has n>3t, r=3t+3, and m=2, and it is asymptotically optimal in all three quality parameters while using the optimal number of processors. Using these protocols as building blocks, families of protocols with intermediate quality parameters, offering better tradeoffs than previous results, are obtained. All the protocols work in polynomial time and have succinct descriptions.>
Piotr Berman, Juan A. Garay 0001, Kenneth J. Perry
FOCS1
1989 Asymptotically Optimal Distributed Consensus (Extended Abstract)
Piotr Berman, Juan A. Garay 0001
ICALP1
1989 Efficient Agreement on Bounded-Degree Networks
Piotr Berman, Juan A. Garay 0001
ICPP (1)1
1989 On the Complexity of Approximating the Independent Set Problem
Piotr Berman, Georg Schnitger
STACS1
1988 Investigations of Fault-Tolerant Networks of Computers (Preliminary Version)
abstract
Article Free Access Share on Investigations of fault-tolerant networks of computers Authors: Piotr Berman Department of Computer Science, The Pennsylvania State University Department of Computer Science, The Pennsylvania State UniversityView Profile , J'anos Simon Department of Computer Science, The University of Chicago Department of Computer Science, The University of ChicagoView Profile Authors Info & Claims STOC '88: Proceedings of the twentieth annual ACM symposium on Theory of computingJanuary 1988 Pages 66–77https://doi.org/10.1145/62212.62219Online:01 January 1988Publication History 10citation258DownloadsMetricsTotal Citations10Total Downloads258Last 12 Months16Last 6 weeks2 Get Citation AlertsNew Citation Alert added!This alert has been successfully added and will be sent to:You will be notified whenever a record that you have chosen has been cited.To manage your alert preferences, click on the button below.Manage my AlertsNew Citation Alert!Please log in to your account Save to BinderSave to BinderCreate a New BinderNameCancelCreateExport CitationPublisher SiteeReaderPDF
Piotr Berman, Janos Simon
STOC1
1987 Learning One-Counter Languages in Polynomial Time (Extended Abstract)
abstract
We demonstrate that the class of languages accepted by deterministic one-counter machines, or DOCAs (a natural subset of the context-free languages), is learnable in polynomial time. Our learning protocol is based upon Angluin's concept of a "minimally adequate teacher" who can answer membership queries about a concept and provide counterexamples to incorrect hypothesized concepts. We also demonstrate that the problem of testing DOCAs for equivalence may be solved in polynomial time, answering a question posed by Valiant and Paterson.
Piotr Berman, Robert Roos
FOCS1
1987 A Learning Algorithm for a Class of Context-Free Languages (Extended Abstract)
Piotr Berman, Robert Roos
ISMIS1
1983 Deterministic Dynamic Logic of Recursive Programs is Weaker than Dynamic Logic
Piotr Berman
FCT1
1983 Lower Bounds on Graph Threading by Probabilistic Machines (Preliminary Version)
abstract
It is likely that reliable and fast space-bounded probabilistic acceptors are less powerful than nondeterministic ones. We consider a restricted model of space-bounded probabilistic computation, the random analog of a model studied in [CR]. We show that maze traversal (a complete problem for nondeterministic space log n) requires space Ω(log2n/loglogn) by random machines, even if 'fast' is relaxed to mean only 'subexponential'. In particular, the lower bound on space holds for the time complexity of Savitch's algorithm (which can be simulated in the model).
Piotr Berman, Janos Simon
FOCS1
1982 On the Power of Nondeterminism in Dynamic Logic
Piotr Berman, Joseph Y. Halpern, Jerzy Tiuryn
ICALP1
1980 A Note on Sweeping Automata
Piotr Berman
ICALP1
1978 Relationship Between Density and Deterministic Complexity of NP-Complete Languages
Piotr Berman
ICALP1