ppxscal/embedding_network huggingface dataset:
Reconstructing distances in physical maps of chromosomes with nonoverlapping probes
Authors: John Krececioglu, Sanjay Shete, Jonathan Arnold
Venue: Proceedings of the fourth annual international conference on Computational molecular biology (2000)

We present a new method for reconstructing the distances between probes in physical maps of chromosomes constructed by hybridizing pairs of clones under the so-called sampling-without-replacement protocol. In this protocol, which is simple, inexpensive, and has been used to successfully map several organisms, equal-length clones are hybridized against a clone-subset called the probes. The probes are chosen by a sequential process that is designed to generate a pairwise-nonoverlapping subset of the clones. We derive a likelihood function on probe spacings and orders for this protocol under a natural model of hybridization error, and describe how to reconstruct the most likely spacing for a given order under this objective using continuous optimization. The approach is tested on simulated data and real data from chromosome VI of Aspergillus nidulans. On simulated data we recover the true order and close to the true spacing; on the real data, for which the true order and spacing is unknown, we recover a probe order differing significantly from the published one. To our knowledge this is the first practical approach for computing a globally-optimal maximum-likelihood reconstruction of interprobe distances from clone-probe hybridization data.
Harp: a distributed query system for legacy public libraries and structured databases
Authors: Ee-Peng Lim, Ying Lu
Venue: ACM Transactions on Information Systems (TOIS) (1999)

The main purpose of a digital library is to facilitate users easy access to enormous amount of globally networked information. Typically, this information includes preexisting public library catalog data, digitized document collections, and other databases. In this article, we describe the distributed query system of a digital library prototype system known as HARP. In the HARP project, we have designed and implemented a distributed query processor and its query front-end to support integrated queries to preexisting public library catalogs and structured databases. This article describes our experiences in the design of an extended Sequel (SQL) query language known as HarpSQL. It also presents the design and implementation of the distributed query system. Our experience in distributed query processor and user interface design and development will be highlighted. We believe that our prototyping effort will provide useful lessons to the development of a complete digital library infrastructure.
Multicast snooping: a new coherence method using a multicast address network
Authors: E. Ender Bilir, Ross M. Dickson, Ying Hu, Manoj Plakal, Daniel J. Sorin, Mark D. Hill, David A. Wood
Venue: ACM SIGARCH Computer Architecture News (1999)

This paper proposes a new coherence method called "multicast snooping" that dynamically adapts between broadcast snooping and a directory protocol. Multicast snooping is unique because processors predict which caches should snoop each coherence transaction by specifying a multicast "mask." Transactions are delivered with an ordered multicast network, such as an Isotach network, which eliminates the need for acknowledgment messages. Processors handle transactions as they would with a snooping protocol, while a simplified directory operates in parallel to check masks and gracefully handle incorrect ones (e.g., previous owner missing). Preliminary performance numbers with mostly SPLASH-2 benchmarks running on 32 processors show that we can limit multicasts to an average of 2-6 destinations ( lt; lt; 32) and we can deliver 2-5 multicasts per network cycle ( gt; gt; broadcast snooping's 1 per cycle). While these results do not include timing, they do provide encouragement that multicast snooping can obtain data directly (like broadcast snooping) but apply to larger systems (like directories).
Using the exact state space of a Markov model to compute approximate stationary measures
Authors: Andrew S. Miner, Gianfranco Ciardo, Susanna Donatelli
Venue: Proceedings of the 2000 ACM SIGMETRICS international conference on Measurement and modeling of computer systems (2000)

We present a new approximation algorithm based on an exact representation of the state space S, using decision diagrams, and of the transition rate matrix R, using Kronecker algebra, for a Markov model with K submodels. Our algorithm builds and solves K Markov chains, each corresponding to a different aggregation of the exact process, guided by the structure of the decision diagram, and iterates on their solution until their entries are stable. We prove that exact results are obtained if the overall model has a product-form solution. Advantages of our method include good accuracy, low memory requirements, fast execution times, and a high degree of automation, since the only additional information required to apply it is a partition of the model into the K submodels. As far as we know, this is the first time an approximation algorithm has been proposed where knowledge of the exact state space is explicitly used.
A General Class of Greedily Solvable Linear Programs
Authors: Maurice Queyranne, Frits Spieksma, Fabio Tardella
Venue: Mathematics of Operations Research (1998)

A greedy algorithm solves a dual pair of linear programs where the primal variables are associated to the elements of a sublattice B of a finite product lattice, and the cost coefficients define a submodular function on B. This approach links and generalizes two well-known classes of greedily solvable linear programs. The primal problem generalizes the (ordinary and multi-index) transportation problems satisfying a Monge condition (Hoffman 1963; Bein et al. 1995) to the case of forbidden cells where the nonforbidden cells form a sublattice. The dual problem generalizes to an arbitrary finite product lattice the linear optimization problem over submodular polyhedra (Lovasz 1983; Fujishige and Tomizawa 1983), which stemmed from the work of Edmonds (1970) on polymatroids. Our model and results also encompass the dual pairs of linear programs and their greedy solutions defined by Lovasz (1983) for the special case of the Boolean algebra, and by Faigle and Kern (1996) for the case of so-called "rooted forests." We also discuss relationships between Monge properties and submodularity, and present a class of problems with submodular costs arising in production and logistics.
Transforming cabbage into turnip: polynomial algorithm for sorting signed permutations by reversals
Authors: Sridhar Hannenhalli, Pavel A. Pevzner
Venue: Journal of the ACM (JACM) (1999)

Genomes frequently evolve by reversals &rgr;(i,j) that transform a gene order &pgr;1 &hellip; &pgr;i&pgr;i+1 &hellip; &pgr;j-1&pgr;j &hellip; &pgr;n into &pgr;1 &hellip; &pgr;i&pgr;j-1 &hellip; &pgr;i+1&pgr;j &hellip; &pgr;n. Reversal distance between permutations &pgr; and &sgr;is the minimum number of reversals to transform &pgr; into &Agr;. Analysis of genome rearrangements in molecular biology started in the late 1930's, when Dobzhansky and Sturtevant published a milestone paper presenting a rearrangement scenario with 17 inversions between the species of Drosophilia. Analysis of genomes evolving by inversions leads to a combinatorial problem of sorting by reversals studied in detail recently. We study sorting of signed permutations by reversals, a problem that adequately models rearrangements in a small genomes like chloroplast or mitochondrial DNA. The previously suggested approximation algorithms for sorting signed permutations by reversals compute the reversal distance between permutations with an astonishing accuracy for both simulated and biological data. We prove a duality theorem explaining this intriguing performance and show that there exists a &ldquo;hidden&rdquo; parameter that allows one to compute the reversal distance between signed permutations in polynomial time.
An adaptive query execution system for data integration
Authors: Zachary G. Ives, Daniela Florescu, Marc Friedman, Alon Levy, Daniel S. Weld
Venue: Proceedings of the 1999 ACM SIGMOD international conference on Management of data (1999)

Query processing in data integration occurs over network-bound, autonomous data sources. This requires extensions to traditional optimization and execution techniques for three reasons: there is an absence of quality statistics about the data, data transfer rates are unpredictable and bursty, and slow or unavailable data sources can often be replaced by overlapping or mirrored sources. This paper presents the Tukwila data integration system, designed to support adaptivity at its core using a two-pronged approach. Interleaved planning and execution with partial optimization allows Tukwila to quickly recover from decisions based on inaccurate estimates. During execution, Tukwila uses adaptive query operators such as the double pipelined hash join, which produces answers quickly, and the dynamic collector, which robustly and efficiently computes unions across overlapping data sources. We demonstrate that the Tukwila architecture extends previous innovations in adaptive execution (such as query scrambling, mid-execution re-optimization, and choose nodes), and we present experimental evidence that our techniques result in behavior desirable for a data integration system.
Information Systems' Approaches and Designs and Facility Information: Survey of Acute Care Hospitals in the United States
Authors: Myron Hatcher
Venue: Journal of Medical Systems (1998)

These survey results are based on a national survey of acute care hospitals. A random sample of 813 hospitals was selected with 115 responding and 33 incorrect address returns resulting in a 15% response rate. The purpose of the study was to measure the extent of information systems integration in the financial, medical, and administrative systems of the hospitals. The rate of adoption of information technology or technology transfer is discussed. Facility demographics are presented. Characteristics of information systems' approaches and designs are reviewed and their implications discussed. This information will provide benchmarks for hospitals to determine their information systems position and to set goals.
Numerical Solutions of a Nonlinear Evolution System with Small Dissipation on Parallel Processors
Authors: Chung-Chiang Chou, Yuefan Deng
Venue: Journal of Scientific Computing (1998)

A nonlinear evolution system constructed from the Lorenz system is solved numerically by a parallelized predictor-corrector method. The numerical solution of such system reveals the details of interactions between dissipation and ellipticity and it may lead to better understanding of instability in some physical systems. Our algorithm and its implementation for solving this system is of general use for the study of strictly nonlinear parabolic equations.
On the Radius-Edge Condition in the Control Volume Method
Authors: Gary L. Miller, Dafna Talmor, Shang-Hua Teng, Noel Walkington
Venue: SIAM Journal on Numerical Analysis (1999)

In this paper we show that the control volume algorithm for the solution of Poisson's equation in three dimensions will converge even if the mesh contains a class of very flat tetrahedra (slivers). These tetrahedra are characterized by the fact that they have modest ratios of diameter to shortest edge, but large circumscribing to inscribed sphere radius ratios, and therefore may have poor interpolation properties. Elimination of slivers is a notoriously difficult problem for automatic mesh generation algorithms. We also show that a discrete Poincar&eacute; inequality will continue to hold in the presence of slivers.
A Practical Scheduling Method for Multiclass Production Systems with Setups
Authors: Feng Cheng, Suresh P. Sethi, Tava Lennon Olsen
Venue: Management Science (1999)

Consider a multiclass production system where many job classes share a single server and a setup time is incurred whenever the server changes class. This paper presents a simple method for scheduling these systems that performs well, not only with respect to mean waiting time, but also with respect to waiting-time variance and the outer percentiles of waiting time. The scheduling method is dynamic and uses the ages of items in each queue, as well as the queue statistics, to decide which queue to service next.
Connectivity on Complete Lattices
Authors: Jean Serra
Venue: Journal of Mathematical Imaging and Vision (1998)

Classically, connectivity is a topological notion for sets, often introduced by means of arcs. A nontopological axiomatics has been proposed by Matheron and Serra. The present paper extends it to complete sup-generated lattices. A connection turns out to be characterized by a family of openings labelled by the sup-generators, which partition each element of the lattice into maximal terms, of zero infima. When combined with partition closings, these openings generate strong sequential alternating filters. Starting from a first connection several others may be designed by acting on some dilations or symmetrical operators. When applying this theory to function lattices, one interprets the so-called connected operators in terms of actual connections, as well as the watershed mappings. But the theory encompasses the numerical functions and extends, among others, to multivariate lattices.
Dual-VT SRAM cells with full-swing single-ended bit line sensing for high-performance on-chip cache in 0.13 μm technology generation
Authors: Fatih Hamzaoglu, Yibin Te, Ali Keshavarzi, Kevin Zhang, Siva Narendra, Shekhar Borkar, Mircea Stan, Vivek De
Venue: Proceedings of the 2000 international symposium on Low power electronics and design (2000)

Comparisons among different dual-VT design choices for a large on-chip cache with single-ended sensing show that the design using a dual-VT cell and low-VT peripheral circuits is the best, and provides 10% performance gain with 1.2x larger active leakage power, and 1.6% larger cell area compared to the best design using high-VT cells.
Memory system energy (poster session): influence of hardware-software optimizations
Authors: G. Esakkimuthu, N. Vijaykrishnan, M. Kandemir, M. J. Irwin
Venue: Proceedings of the 2000 international symposium on Low power electronics and design (2000)

Memory system usually consumes a significant amount of energy in many battery-operated devices. In this paper, we provide a quantitative comparison and evaluation of the interaction of two hardware cache optimization mechanisms (block buffering and sub-banking) and three widely used compiler optimization techniques (linear loop transformation, loop tiling, and loop unrolling). Our results show that the pure hardware optimizations (eight block buffers and four sub-banks in a 4K, 2-way cache) provided up to 4% energy saving, with an average saving of 2% across all benchmarks. In contrast, the pure software optimization approach that uses all three compiler optimizations, provided at least 23% energy saving, with an average of 62%. However, a closer observation reveals that hardware optimization becomes more critical for on-chip cache energy reduction when executing optimized codes.
Evolutionary design of complex software (EDCS) demonstration days 1999
Authors: Wayne Stidolph
Venue: ACM SIGSOFT Software Engineering Notes (2000)

This report summarizes the Product/Technology demonstrations given at Defense Advanced Research Projects Agency (DARPA) Evolutionary Design of Complex Software (EDCS) Program Demonstration Days, held 28-29 June 1999 at the Sheraton National Hotel, Arlington, VA.
Student paper competition (abstract only)
Authors: Sara Basse, Jean Camp, Dan Gillmor, Wiley Hodges, Bruce Umbaugh, Danny Yee
Venue: Proceedings of the tenth conference on Computers, freedom and privacy: challenging the assumptions (2000)

The top three papers from the CFP 2000 student paper competition have been printed in this proceedings. They are: Internet filter effectiveness: testing over and underinclusive blocking decisions of four popular filters Christopher D. Hunter Pages 287-294 When social meets technical: ethics and the design of "social" technologies Patrick Feng Pages 295-301 Quantum "encryption" Mark V. Hurwitz Pages 303-313
Java servlet programming
Authors: Jason Hunter, William Crawford
Venue:  (1998)

Java servlets offer a fast, powerful, portable replacement for CGI scripts. Java Servlet Programming covers everything you need to know to write effective servlets. Topics include: serving dynamic Web content, maintaining state information, session tracking, database connectivity using JDBC, and applet-servlet communication.
Software Agent-Oriented Frameworks for Global Query Processing
Authors: Zakaria Maamar, Bernard Moulin, Gilbert Babin, Yvan Bédard
Venue: Journal of Intelligent Information Systems (1999)

The paper introduces the concept of software agent-oriented frameworks for global query processing in an interoperable environment. Such an environment is developed for the purpose of making cooperative interactions between several systems. These latter are distributed on networks and may present several incompatibilities. The global query processing is applied to the SIGAL project which aims at developing an interoperable environment for georeferenced digital libraries. This environment provides users with services that will free them from worrying about information distribution and disparities.
A computing research repository: why not solve the problems first?
Authors: A. J. van Loon
Venue: ACM Journal of Computer Documentation (JCD) (2000)

The Computing Research Repository (CoRR) described by Halpern is potentially a powerful tool for researchers in computing science.In its current form, however, shortcomings exist that restrict its value and that,in the long term,might strongly undermine its usefulness.Important aspects that have insufficiently been taken care of are (1) the quality and consequently the reliability of the material stored, (2) the still restricted submission of material,which implies that other sources have to be consulted by researchers as well, (3) the still unsound financial basis of the project, and (4) the confusion that may easily arise when a preliminary version is stored in the CoRR, while a different final version is published in a journal.
Lattices of Parabolic Subgroups in Connection with Hyperplane Arrangements
Authors: Hélène Barcelo, Edwin Ihrig
Venue: Journal of Algebraic Combinatorics: An International Journal (1999)

Let W be a Coxeter group acting as a matrix group by way of the dual of the geometric representation. Let L be the lattice of intersections of all reflecting hyperplanes associated with the reflections in this representation. We show that L is isomorphic to the lattice consisting of all parabolic subgroups of W. We use this correspondence to find all W for which L is supersolvable. In particular, we show that the only infinite Coxeter group for which L is supersolvable is the infinite dihedral group. Also, we show how this isomorphism gives an embedding of L into the partition lattice whenever W is of type An, Bn or Dn. In addition, we give several results concerning non-broken circuit bases (NBC bases) when W is finite. We show that L is supersolvable if and only if all NBC bases are obtainable by a certain specific combinatorial procedure, and we use the lattice of parabolic subgroups to identify a natural subcollection of the collection of all NBC bases.
Empirical Martingale Simulation for Asset Prices
Authors: Jin-Chuan Duan, Jean-Guy Simonato
Venue: Management Science (1998)

This paper proposes a simple modification to the standard Monte Carlo simulation procedure for computing the prices of derivative securities. The modification imposes the martingale property on the simulated sample paths of the underlying asset price. This procedure is referred to as the empirical martingale simulation (EMS). The EMS ensures that the price estimated by simulation satisfies the rational option pricing bounds. The EMS yields a substantial error reduction for the price estimate and can be easily coupled with the standard variance reduction methods. Simulation studies are conducted for European and Asian call options using both the Black and Scholes and GARCH option pricing frameworks. The results indicate that the EMS yields substantial variance reduction particularly for in- and at-the-money or longer-maturity options. The option price estimate based on the EMS is found to exhibit a minor small-sample bias only in few occasions. An analysis of the trade-off between computing time and price accuracy reveals that the EMS dominates the conventional simulation methods.
Is SC + ILP = RC?
Authors: Chris Gniady, Babak Falsafi, T. N. Vijaykumar
Venue: ACM SIGARCH Computer Architecture News (1999)

Sequential consistency (SC) is the simplest programming interface for shared-memory systems but imposes program order among all memory operations, possibly precluding high performance implementations. Release consistency (RC), however, enables the highest performance implementations but puts the burden on the programmer to specify which memory operations need to be atomic and in program order. This paper shows, for the first time, that SC implementations can perform as well as RC implementations if the hardware provides enough support for speculation. Both SC and RC implementations rely on reordering and overlapping memory operations for high performance. To enforce order when necessary, an RC implementation uses software guarantees, whereas an SC implementation relies on hardware speculation. Our SC implementation, called SC++, closes the performance gap because: (1) the hardware allows not just loads, as some current SC implementations do, but also stores to bypass each other speculatively to hide remote latencies, (2) the hardware provides large speculative state for not just processor, as previously proposed, but also memory to allow out-of-order memory operations, (3) the support for hardware speculation does not add excessive overheads to processor pipeline critical paths, and (4) well-behaved applications incur infrequent rollbacks of speculative execution. Using simulation, we show that SC++ achieves an RC implementation's performance in all the six applications we studied.
Boosting superpage utilization with the shadow memory and the partial-subblock TLB
Authors: Cheol Ho Park
Venue: Proceedings of the 14th international conference on Supercomputing (2000)

While superpage is an efficient solution to increase TLB reach, its limited flexibility for address mapping is still a hard issue. Our proposed mechanism has been developed for taking advantage of two previous approaches which resolve the issue partially: the partial-subblock TLB and the shadow memory. Through integration of them, our mechanism enjoys various benefits inherited from the both sides. By adopting Memory Controller TLB (MTLB) from the shadow memory, it allows superpages to be composed of arbitrary physical pages. The entry structure of the partial-subblock TLB applied for the processor TLB enables all invalid address mappings to be identified inside CPU, which reduces the overhead of handling invalid mappings. In addition, cache flushing which is required when a mapping of shadow address to physical address is destroyed (e.g. due to paging) can be replaced just by resetting the corresponding valid bit in the processor TLB. At last, the per-base-page reference bits in the processor TLB make the page replacement policy of the operating system more efficient.In simulation with six benchmarks, our mechanism generates only 27% of TLB misses compared to the single-page-size TLB. With a detailed analysis, it is shown to be evident that the efficiency of our mechanism is magnified in real computing environment where multitasking and applications of large sizes are ordinary cases.