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Dependence of tree copy functions

Lih-Hsing Hsu
1985 Discrete Mathematics  
The graph copy function when restricted to the set of trees or of rooted trees is called the tree copy function or the rooted tree copy function, respectively.  ...  We show that both the set of tree copy functions and the set of rooted tree copy functions are strongly linearly independent.  ...  {c;j TEST} is a base for the algebra generated by {CT/ T is a rooted tree}. 2 . 2 Dependence of tree copy functions Given a tree T, a vertex x is called a brink point if J{y ) deg,(y) = 1, x is adjacent  ... 
doi:10.1016/s0012-365x(85)80004-2 fatcat:uakl4qbrwzch3db6veunejp65e

Efficient incremental evaluation of aggregate values in attribute grammars

Roger Hoover, Tim Teitelbaum
1986 Proceedings of the 1986 SIGPLAN symposium on Compiler contruction - SIGPLAN '86  
Aggregate valued attributes, which store collections of keyed elements, are required in attribute grammars to communicate information from multiple definition sites to multiple use locations.  ...  We present efficient algorithms for incrementally maintaining these aggregate values and give an incremental evaluation algorithm that restricts attribute propagation to attributes dependent only upon  ...  The copy bypass tree for f contains dependency pointers to all nontrivially used copy attributes, which in turn point back to the definition of f at the head of the tree of copy If no copy chains originate  ... 
doi:10.1145/12276.13315 dblp:conf/sigplan/HooverT86 fatcat:mst3snixvjf4de3t74ytx7b6ri

Dynamically bypassing copy rule chains in attribute grammars

Roger Hoover
1986 Proceedings of the 13th ACM SIGACT-SIGPLAN symposium on Principles of programming languages - POPL '86  
Attribute grammars require copy rules to transfer values between attribute instances distant in an attributed parse tree.  ...  We introduce copy bypass attribute propagation that dynamically replaces copy rules with nonlocal dependencies, resulting in f~ster incremental evaluation. .A evaluation strategy is used that approximates  ...  Attributing the parse tree in Figure 2 using the copy bypass semantic function results in the attribute dependency graph shown in Figure 5 .  ... 
doi:10.1145/512644.512646 dblp:conf/popl/Hoover86 fatcat:ztduxpnpcvaa7f7csg3txupvua

A generalized birth and death process for modeling the fates of gene duplication

Jing Zhao, Ashley I. Teufel, David A. Liberles, Liang Liu
2015 BMC Evolutionary Biology  
Starting with a single population corresponding to the lineage of a phylogenetic tree and with an assumption of a clock that starts ticking for each duplicate at its birth, an age-dependent birth-death  ...  evolved and the genes with novel functions arose.  ...  Thus, in the timedependent birth-death model, the loss rate μ t of a gene copy is a function of time t. However, the loss rate μ t should be a function of the ages of gene copies.  ... 
doi:10.1186/s12862-015-0539-2 pmid:26643106 pmcid:PMC4672517 fatcat:pg3yg6gmnzc27lxnae64jzteeq

On Mechanistic Modeling of Gene Content Evolution: Birth-Death Models and Mechanisms of Gene Birth and Gene Retention

Ashley Teufel, Jing Zhao, Malgorzata O'Reilly, Liang Liu, David Liberles
2014 Computation  
Existing models are then extended in deriving two new birth/death models for phylogenetic application in a gene tree/species tree reconciliation framework to enable probabilistic inference of the mechanisms  ...  The goal of this work is to synthesize a detailed discussion of modeling duplicate genes to address biological questions, moving from previous work to future trajectories with the aim of generating better  ...  The subfunctionalization rate is still time heterogeneous, as it is dependent upon the accumulation of deleterious changes across two gene copies that is a function of the number of redundant copies, the  ... 
doi:10.3390/computation2030112 fatcat:xv6zxmrmuzc63e4tfxai2jlpfa

Correction of copy number induced false positives in CRISPR screens [article]

Antoine de Weck, Javad Golji, Michael D. Jones, Joshua M. Korn, Eric Billy, E. Robert McDonald, Tobias Schmelzle, Hans Bitter, Audrey Kauffmann
2017 bioRxiv   pre-print
Cell autonomous cancer dependencies are now routinely identified using CRISPR loss-of-function screens.  ...  The General Additive Model (GAM) method models the screening data as a function of the known copy number values and removes the systematic effect from the measured lethality.  ...  Here, one dimensional regression trees are used to estimate the sensitivity of the guides as a function of the genomic location alone.  ... 
doi:10.1101/151985 fatcat:ognzk7yxmnc4zei6yen4vcpi3i

Detecting Copy Directions among Programs Using Extreme Learning Machines

Bin Wang, Xiaochun Yang, Guoren Wang
2015 Mathematical Problems in Engineering  
We also analyze the features of data dependencies between any original program and its copy program, and based on it we propose a feedback framework to find a good feature space that can achieve both accuracy  ...  Many methods have been proposed to detect plagiarism among programs based on the program dependence graph, a graph representation of a program.  ...  the tree into a sequence of tree nodes to build a suffix tree for similarity matching.  ... 
doi:10.1155/2015/793697 fatcat:gibukq3agfd6xljpcvvv5ftpfu

Parallel Exact Inference on a CPU-GPGPU Heterogenous System

Hyeran Jeon, Yinglong Xia, Viktor K. Prasanna
2010 2010 39th International Conference on Parallel Processing  
In this paper, we design an efficient scheduler hosted by the CPU to allocate cliques in junction trees to the GPGPU at run time.  ...  Our implementation of the proposed method on GPGPU platforms achieved 30× speedup compared with state-of-the-art multicore processors, and it sustains 70% of the theoretical upper bound of the GPGPU throughput  ...  Method of junction tree traversal : The dependencies among cliques in the junction tree limits the number of cliques that can be assigned to a kernel function.  ... 
doi:10.1109/icpp.2010.15 dblp:conf/icpp/JeonXP10 fatcat:4gntmnvifjf2lgzmiffmk2oapm

Storage allocation strategies for recursive attribute evaluators [chapter]

Kazunori Mizushima, Takuya Katayama
1998 Lecture Notes in Computer Science  
A is a set of attributes. Each nonterminal X E VN has a subset A[X] of A. A[X] is a disjoint union of the set INH[X] of inherited attributes, which pass  ...  We call the edge of copy rule a copy edge and call other edges function edges.Let the production rule p : Xo -'+ XtX2...  ...  copy rules are frequently used in multi-cast style dependency.  ... 
doi:10.1007/bfb0026422 fatcat:hvkiuqb76jeoxbo3rbino7k5wu

Page 5315 of Mathematical Reviews Vol. , Issue 82m [page]

1982 Mathematical Reviews  
Functional dependencies of the form X— a(R)—where X’»a(R) for all X’ C X—are called key dependencies. Other kinds of dependencies are multivalued dependencies, join dependencies, etc.  ...  The projection on X of R is 7y(R)={ty|tER}. There are many kinds of dependencies. Among these we have functional dependencies (FD’s) (XY meaning that, for all ¢,t’ER, ty=ty implies ty=r}).  ... 

Loop Optimization Framework [article]

Michael Kruse, Hal Finkel
2018 arXiv   pre-print
Each transformation can make use of a common infrastructure such as dependency analysis, transformation preconditions, etc.  ...  The LLVM compiler framework supports a selection of loop transformations such as vectorization, distribution and unrolling.  ...  Department of Energy organizations (Office of Science and the National Nuclear Security Administration) responsible for the planning and preparation of a capable exascale ecosystem, including software,  ... 
arXiv:1811.00632v1 fatcat:332g4mtcr5gktk66xgsfclqvcy

Space Optimized Multicast in Delay Tolerant Networks

Anshuman Tripathi
2013 International Journal of Computing and Network Technology  
The proposed algorithm has been simulated on SLAW mobility model and shows a reduction in the number of copies of message in the network by as much as 75% (reducing to ¼ th of the number), compared to  ...  Many multicast protocols for Delay Tolerant Networks fall in the class of tree based algorithms. Most of these tree computations aim to reduce the time taken by the message to reach its recipients.  ...  The main motivation behind this choice of function is that in every iteration, the importance of the nodes that are already in the multicast tree increases as they are selected.  ... 
doi:10.12785/ijcnt/010205 fatcat:quo5wkj3pjhqppyjxzgmwdqhoq

Attribute grammars fly first-class

Marcos Viera, S. Doaitse Swierstra, Wouter Swierstra
2009 Proceedings of the 14th ACM SIGPLAN international conference on Functional programming - ICFP '09  
We present a typed embedding of AG in Haskell satisfying all these requirements.  ...  The paper presents a realistic example of type-class-based type-level programming in Haskell.  ...  Another complication is that the interfaces of non-terminals are in general not uniform, thus necessitating all kind of tricks to change the monad at the right places, keeping information to be reused  ... 
doi:10.1145/1596550.1596586 dblp:conf/icfp/VieraSS09 fatcat:hrutua36avbobbqlthz34wnxfm

Attribute grammars fly first-class

Marcos Viera, S. Doaitse Swierstra, Wouter Swierstra
2009 SIGPLAN notices  
We present a typed embedding of AG in Haskell satisfying all these requirements.  ...  The paper presents a realistic example of type-class-based type-level programming in Haskell.  ...  Acknowledgments We want to thank Oege de Moor for always lending an ear in discussing the merits of attribute grammars, and how to further profit from them.  ... 
doi:10.1145/1631687.1596586 fatcat:pdlbtpr2mzbjtpmwuunxo56k44

Generalising Tree Traversals to DAGs

Patrick Bahr, Emil Axelsson
2015 Proceedings of the 2015 Workshop on Partial Evaluation and Program Manipulation - PEPM '15  
Our recursion scheme allows the programmer to implement a tree traversal and then apply it to compact graph representations of trees instead.  ...  We present a recursion scheme based on attribute grammars that can be transparently applied to trees and acyclic graphs.  ...  Copying Attribute Grammars At first we consider the case of copying AGs, i.e.  ... 
doi:10.1145/2678015.2682539 dblp:conf/pepm/BahrA15 fatcat:rbdztkdunzdevadpfaruxnogdm
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