From Micro to Macro: How the Overlap Graph Determines the Reduction Graph in Ciliates

Author(s):  
Robert Brijder ◽  
Hendrik Jan Hoogeboom ◽  
Grzegorz Rozenberg
Keyword(s):  
2021 ◽  
Vol 178 (3) ◽  
pp. 173-185
Author(s):  
Arthur Adinayev ◽  
Itamar Stein

In this paper, we study a certain case of a subgraph isomorphism problem. We consider the Hasse diagram of the lattice Mk (the unique lattice with k + 2 elements and one anti-chain of length k) and find the maximal k for which it is isomorphic to a subgraph of the reduction graph of a given one-rule string rewriting system. We obtain a complete characterization for this problem and show that there is a dichotomy. There are one-rule string rewriting systems for which the maximal such k is 2 and there are cases where there is no maximum. No other intermediate option is possible.


2018 ◽  
Vol 48 (3) ◽  
pp. 729-751
Author(s):  
Saeid Bagheri ◽  
Fatemeh Nabaei ◽  
Rashid Rezaeii ◽  
Karim Samei
Keyword(s):  

2003 ◽  
Vol 150 (1-2) ◽  
pp. 59-95 ◽  
Author(s):  
L.Karl Branting

2018 ◽  
Vol 28 ◽  
Author(s):  
ERIC L. SEIDEL ◽  
RANJIT JHALA ◽  
WESTLEY WEIMER

AbstractStatic type errors are a common stumbling block for newcomers to typed functional languages. We present a dynamic approach to explaining type errors by generating counterexample witness inputs that illustrate how an ill-typed program goes wrong. First, given an ill-typed function, we symbolically execute the body to synthesize witness values that make the program go wrong. We prove that our procedure synthesizes general witnesses in that if a witness is found, then for all inhabited input types, there exist values that can make the function go wrong. Second, we show how to extend this procedure to produce a reduction graph that can be used to interactively visualize and debug witness executions. Third, we evaluate the coverage of our approach on two data sets comprising over 4,500 ill-typed student programs. Our technique is able to generate witnesses for around 85% of the programs, our reduction graph yields small counterexamples for over 80% of the witnesses, and a simple heuristic allows us to use witnesses to locate the source of type errors with around 70% accuracy. Finally, we evaluate whether our witnesses help students understand and fix type errors, and find that students presented with our witnesses show a greater understanding of type errors than those presented with a standard error message.


2009 ◽  
Vol 20 (02) ◽  
pp. 271-291 ◽  
Author(s):  
ROBERT BRIJDER ◽  
HENDRIK JAN HOOGEBOOM ◽  
GRZEGORZ ROZENBERG

Ciliates are unicellular organisms having two types of functionally different nuclei: micronucleus and macronucleus. Gene assembly transforms a micronucleus into a macronucleus, thereby transforming each gene from its micronuclear form to its macronuclear form. Within a formal intramolecular model of gene assembly based on strings, the notion of reduction graph represents the macronuclear form of a gene, including byproducts, given only a description of the micronuclear form of that gene. For a more abstract model of gene assembly based on graphs, one cannot, in general, define the notion of reduction graphs. We show that if we restrict ourselves to the so-called realistic overlap graphs (which correspond to genes occurring in nature), then the notion of reduction graph can be defined in a manner equivalent to the string model. This allows one to carry over from the string model to the graph model several results that rely on the notion of reduction graph.


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