8623199
Calculating accumulations
Theaccumulation strategy consists of generalizing a function over an algebraic data structure by inclusion of an extra parameter, anaccumulating parameter, for reusing and propagating intermediate results. However, there remain two major difficulties in this accumulation strategy. One is to determinewhere andwhen to generalize the original function. The other, surprisingly not yet receiving its worthy consideration, is how to manipulate accumulations. To overcome these difficulties, we propose to formulate accumulations ashigher order catamorphisms, and provide several general transformation rules for calculating accumulations (i.e., finding and manipulating accumulations) bycalculation-based (rather than a search-based) program transformation methods. Some examples are given for illustration.
13526098
Systematic Derivation of Tree Contraction Algorithms
While tree contraction algorithms play an important role in efficient tree computation in parallel, it is difficult to develop such algorithms due to the strict conditions imposed on contracting op...
15997088
A New Parallel Skeleton for General Accumulative Computations
Skeletal parallel programming enables programmers to build a parallel program from ready-made components (parallel primitives) for which efficient implementations are known to exist, making both the parallel program development and the parallelization process easier. Constructing efficient parallel programs is often difficult, however, due to difficulties in selecting a proper combination of parallel primitives and in implementing this combination without having unnecessary creations and exchanges of data among parallel primitives and processors. To overcome these difficulties, we propose a powerful and general parallel skeleton, accumulate, which can be used to naturally code efficient solutions to problems as well as be efficiently implemented in parallel using Message Passing Interface (MPI).
21046907
Construction of List Homomorphisms by Tupling and Fusion
List homomorphisms are functions which can be efficiently computed in parallel since they ideally suit the divide- sand-conquer paradigm. However, some interesting functions, e.g., the maximum segment sum problem, are not list homomorphisms. In this paper, we propose a systematic way of embedding them into list homomorphisms so that parallel programs are derived. We show, with an example, how a simple, and “obviously” correct, but possibly inefficient solution to the problem can be successfully turned into a semantically equivalent almost homomorphism by means of two transformations: tupling and fusion.
5453797
List Homomorphism with Accumulation
This paper introduces accumulation into list homomorphisms for systematic development of both efficient and correct parallel programs. New parallelizable recursive pattern called H-homomorphism is given, and transformations from sequential patterns in the H-form and Hform into (H-)homomorphism are shown. We illustrate the power of our formalization by developing a novel and general parallel program for a class of interesting and challenging problems, known as maximum marking problems.
17460651
A calculational fusion system HYLO
Fusion, one of the most useful transformation tactics for deriving efficient programs, is the process whereby separate pieces of programs are fused into a single one, leading to an efficient program without intermediate data structures produced. In this paper, we report our on-going investigation on the design and implementation of an automatic transformation system HYLO which performs fusion transformation in a more systematic and more general way than any other systems. The distinguished point of our system is its calculational feature based on simple application of transformation laws rather than traditional search-based transformations.
205878836
A generalization of fan's condition and forbidden subgraph conditions for hamiltonicity
Abstract Let G be a 2-connected graph with n vertices and H be an induced subgraph of G. Denote V0 ≔ {v ϵ V(G): d(v) ⩾ n/2}. If there exists a pair of vertices x and y at distance 2 in H such that {x, y} ⊆ V(H)βV0, then H is called degree light. Let F be the unique graph with degree sequence (1, 1, 1, 3, 3, 3). In this paper, we prove that if G contains no degree light K1, 3 and every degree light F of G contains no induced P4 of G − V0, then G is hamiltonian.
471313
Dependence network modeling for biomarker identification
MOTIVATION
Our purpose is to develop a statistical modeling approach for cancer biomarker discovery and provide new insights into early cancer detection. We propose the concept of dependence network, apply it for identifying cancer biomarkers, and study the difference between the protein or gene samples from cancer and non-cancer subjects based on mass-spectrometry (MS) and microarray data.


RESULTS
Three MS and two gene microarray datasets are studied. Clear differences are observed in the dependence networks for cancer and non-cancer samples. Protein/gene features are examined three at one time through an exhaustive search. Dependence networks are constructed by binding triples identified by the eigenvalue pattern of the dependence model, and are further compared to identify cancer biomarkers. Such dependence-network-based biomarkers show much greater consistency under 10-fold cross-validation than the classification-performance-based biomarkers. Furthermore, the biological relevance of the dependence-network-based biomarkers using microarray data is discussed. The proposed scheme is shown promising for cancer diagnosis and prediction.


AVAILABILITY
See supplements: http://dsplab.eng.umd.edu/~genomics/dependencenetwork/
7795322
The Protein Information Resource
The Protein Information Resource (PIR) is an integrated public resource of protein informatics that supports genomic and proteomic research and scientific discovery. PIR maintains the Protein Sequence Database (PSD), an annotated protein database containing over 283 000 sequences covering the entire taxonomic range. Family classification is used for sensitive identification, consistent annotation, and detection of annotation errors. The superfamily curation defines signature domain architecture and categorizes memberships to improve automated classification. To increase the amount of experimental annotation, the PIR has developed a bibliography system for literature searching, mapping, and user submission, and has conducted retrospective attribution of citations for experimental features. PIR also maintains NREF, a non-redundant reference database, and iProClass, an integrated database of protein family, function, and structure information. PIR-NREF provides a timely and comprehensive collection of protein sequences, currently consisting of more than 1 000 000 entries from PIR-PSD, SWISS-PROT, TrEMBL, RefSeq, GenPept, and PDB. The PIR web site (http://pir.georgetown.edu) connects data analysis tools to underlying databases for information retrieval and knowledge discovery, with functionalities for interactive queries, combinations of sequence and text searches, and sorting and visual exploration of search results. The FTP site provides free download for PSD and NREF biweekly releases and auxiliary databases and files.
3724518
Long Cycles through a Linear Forest
For a graph G and an integer k?1, let S(G)={x?V(G):dG(x)=0} and ?k(G)=min{?ki=1dG(vi):{v1, v2, ?, vk} is an independent set of G}. The main result of this paper is as follows. Let k?3, m?0, and 0?s?k?3. Let G be a (m+k?1)-connected graph and let F be a subgraph of G with |E(F)|=m and |S(F)|=s. If every component of F is a path, then G has a cycle of length ?min{|V(G)|, 2k?k(G)?m} passing through E(F)?V(F). This generalizes three related results known previously.
14260384
Perfect Circular Arc Coloring
The circular arc coloring problem is to find a minimum coloring of a set of arcs of a circle so that no two overlapping arcs share a color. This NP-hard problem arises in a rich variety of applications and has been studied extensively. In this paper we present an O(n2m) combinatorial algorithm for optimally coloring any set of arcs that corresponds to a perfect graph, and propose a new approach to the general circular arc coloring problem.