Metabolic networks represent the relationship between chemical reactions and compounds in cells. In useful metabolite production using microorganisms, it is often required to calculate reaction deletion strategies from the original network to result in growth coupling, which means the target metabolite production and cell growth are simultaneously achieved. Although simple elementary flux mode (EFM)-based methods are useful for listing such reaction deletions strategies, the number of cases to be considered is often proportional to the exponential function of the size of the network. Therefore, it is desirable to develop methods of narrowing down the number of reaction deletion strategy candidates. In this study, the author introduces the idea of L1 norm minimal modes to consider metabolic flows whose L1 norms are minimal to satisfy certain criteria on growth and production, and developed a fast metabolic design listing algorithm based on it (minL1-FMDL), which works in polynomial time. Computational experiments were conducted for (1) a relatively small network to compare the performance of minL1-FMDL with that of the simple EFM-based method and (2) a genome-scale network to verify the scalability of minL1-FMDL. In the computational experiments, it was seen that the average value of the target metabolite production rates of minL1-FMDL was higher than that of the simple EFM-based method, and the computation time of minL1-FMDL was fast enough even for genome-scale networks. The developed software, minL1-FMDL, implemented in MATLAB, is available on https://sunflower.kuicr.kyoto-u.ac.jp/~tamura/software, and can be used for genome-scale metabolic network design for metabolite production.

This paper introduces the maximization version of the k-path vertex cover problem, called the MAXIMUM K-PATH VERTEX COVER problem (MaxPkVC for short): A path consisting of k vertices, i.e., a path of length k-1 is called a k-path. If a k-path Pk includes a vertex v in a vertex set S, then we say that v or S covers Pk. Given a graph G=(V, E) and an integer s, the goal of MaxPkVC is to find a vertex subset S⊆V of at most s vertices such that the number of k-paths covered by S is maximized. The problem MaxPkVC is generally NP-hard. In this paper we consider the tractability/intractability of MaxPkVC on subclasses of graphs. We prove that MaxP3VC remains NP-hard even for split graphs. Furthermore, if the input graph is restricted to graphs with constant bounded treewidth, then MaxP3VC can be solved in polynomial time.

The k-edge-connectivity augmentation problem for a specified set of vertices (kECA-SV for short) is defined by “Given a graph G=(V, E) and a subset Γ ⊆ V, find a minimum set E' of edges such that G'=(V, E ∪ E') has at least k edge-disjoint paths between any pair of vertices in Γ.” Let σ be the edge-connectivity of Γ (that is, G has at least σ edge-disjoint paths between any pair of vertices in Γ). We propose an algorithm for (σ+1)ECA-SV which is done in O(|Γ|) maximum flow operations. Then the time complexity is O(σ2|Γ||V|+|E|) if a given graph is sparse, or O(|Γ||V||BG|log(|V|2/|BG|)+|E|) if dense, where |BG| is the number of pairs of adjacent vertices in G. Also mentioned is an O(|V||E|+|V|2 log |V|) time algorithm for a special case where σ is equal to the edge-connectivity of G and an O(|V|+|E|) time one for σ ≤ 2.

A term is a connected acyclic graph (unrooted unordered tree) pattern with structured variables, which are ordered lists of one or more distinct vertices. A variable of a term has a variable label and can be replaced with an arbitrary tree by hyperedge replacement according to the variable label. The dimension of a term is the maximum number of vertices in the variables of it. A term is said to be linear if each variable label in it occurs exactly once. Let T be a tree and t a linear term. In this paper, we study the graph pattern matching problem (GPMP) for T and t, which decides whether or not T is obtained from t by replacing variables in t with some trees. First we show that GPMP for T and t is NP-complete if the dimension of t is greater than or equal to 4. Next we give a polynomial time algorithm for solving GPMP for a tree of bounded degree and a linear term of bounded dimension. Finally we show that GPMP for a tree of arbitrary degree and a linear term of dimension 2 is solvable in polynomial time.

Response property is a kind of liveness property. Response property problem is defined as follows: Given two activities α and β, whenever α is executed, is β always executed after that? In this paper, we tackled the problem in terms of Workflow Petri nets (WF-nets for short). Our results are (i) the response property problem for acyclic WF-nets is decidable, (ii) the problem is intractable for acyclic asymmetric choice (AC) WF-nets, and (iii) the problem for acyclic bridge-less well-structured WF-nets is solvable in polynomial time. We illustrated the usefulness of the procedure with an application example.

A cograph (complement reducible graph) is a graph which can be generated by disjoint union and complement operations on graphs, starting with a single vertex graph. Cographs arise in many areas of computer science and are studied extensively. With the goal of developing an effective data mining method for graph structured data, in this paper we introduce a graph pattern expression, called a cograph pattern, which is a special type of cograph having structured variables. Firstly, we show that a problem whether or not a given cograph pattern g matches a given cograph G is NP-complete. From this result, we consider the polynomial time learnability of cograph pattern languages defined by cograph patterns having variables labeled with mutually different labels, called linear cograph patterns. Secondly, we present a polynomial time matching algorithm for linear cograph patterns. Next, we give a polynomial time algorithm for obtaining a minimally generalized linear cograph pattern which explains given positive data. Finally, we show that the class of linear cograph pattern languages is polynomial time inductively inferable from positive data.

The k-edge-connectivity augmentation problem with multipartition constraints (kECAMP, for short) is defined by “Given a multigraph G=(V,E) and a multipartition π={V1,...,Vr} (r≥2) of V, that is, $V = igcup_{h = 1}^r V_h$ and Vi∩Vj=∅ (1≤i

This paper deals with a problem to decide whether a given graph structure appears as a pattern in the structure of a given graph. A graph pattern is a triple p=(V,E,H), where (V,E) is a graph and H is a set of variables, which are ordered lists of vertices in V. A variable can be replaced with an arbitrary connected graph by a kind of hyperedge replacements. A substitution is a collection of such replacements. The graph pattern matching problem (GPMP) is the computational problem to decide whether or not a given graph G is obtained from a given graph pattern p by a substitution. In this paper, we show that GPMP for a graph pattern p and a graph G is solvable in polynomial time if the length of every variable in p is 2, p is of bounded treewidth, and G is connected.

An efficient means of learning tree-structural features from tree-structured data would enable us to construct effective mining methods for tree-structured data. Here, a pattern representing rich tree-structural features common to tree-structured data and a polynomial time algorithm for learning important tree patterns are necessary for mining knowledge from tree-structured data. As such a tree pattern, we introduce a term tree pattern t such that any edge label of t belongs to a finite alphabet Λ, any internal vertex of t has ordered children and t has a new kind of structured variable, called a height-constrained variable. A height-constrained variable has a pair of integers (i, j) as constraints, and it can be replaced with a tree whose trunk length is at least i and whose height is at most j. This replacement is called height-constrained replacement. A sequence of consecutive height-constrained variables is called a variable-chain. In this paper, we present polynomial time algorithms for solving the membership problem and the minimal language (MINL) problem for term tree patternshaving no variable-chain. The membership problem for term tree patternsis to decide whether or not a given tree can be obtained from a given term tree pattern by applying height-constrained replacements to all height-constrained variables in the term tree pattern. The MINL problem for term tree patternsis to find a term tree pattern t such that the language generated by t is minimal among languages, generated by term tree patterns, which contain all given tree-structured data. Finally, we show that the class, i.e., the set of all term tree patternshaving no variable-chain, is polynomial time inductively inferable from positive data if |Λ| ≥ 2.

A term tree pattern is a rooted ordered tree pattern which consists of ordered tree structures with edge labels and structured variables with labels. All variables with the same label in a term tree pattern can be simultaneously replaced with ordered trees isomorphic to the same rooted ordered tree. Then, a term tree pattern is suitable for representing structural features common to tree structured data such as XML documents on the web, the secondary structures of RNA in biology and parse trees describing grammatical structures of natural languages. Let $ott$ be the set of all term tree patterns which have one or more variables with the same label. Let $lott$ be the set of all term tree patterns t such that all variables in t have distinct labels. We remark that $lottsubsetneq ott$ holds. In this paper, we consider a problem, called Matching problem for term tree patterns, of deciding whether or not a given rooted ordered tree T is obtained from a given term tree pattern t by replacing variables in t with rooted ordered trees. We show that Matching problem for term tree patterns in $ott$ is NP-complete, by giving a reduction from the string pattern matching problem, which is NP-complete. Next, by giving operations on an interval, which is a set containing all integers between two given integers representing vertex identifiers, we propose an efficient algorithm for solving Matching problem for term tree patterns in $lottsubsetneq ott$. Then, we show that, when an ordered tree having N vertices and a term tree pattern $t in lott$ having n vertices are given, the proposed matching algorithm correctly solves this problem in O(nN) time.

Users of wireless mobile devices need Internet access not only when they stay at home or office, but also when they travel. It may be desirable for such users to select a "longcut route" from their current location to his/her destination that has longer travel time than the shortest route, but provides a better mobile wireless environment. In this paper, we formulate the above situation as the optimization problem of “optimal longcut route selection”, which requires us to find the best route concerning the wireless environment subject to a travel time constraint. For this new problem, we show NP-hardness, propose two pseudo-polynomial time algorithms, and experimental evaluation of the algorithms.

Workflow nets are a standard way for modeling and analyzing workflows. There are two aspects in a workflow: definition and instance. In form of workflow nets, a workflow definition and a workflow instance are respectively represented as a net structure and a marking. The correctness of the workflow definition can be checked by using a workflow nets' property, called soundness. On the other hand, the correctness of the workflow instance can be checked by using a Petri nets' well-known property, called reachability. The reachability problem is known to be intractable. In this paper, we have shown that the reachability problem for (i) sound extended free-choice workflow nets with a marking representing one workflow instance or (ii) acyclic well-structured workflow nets with a marking representing one or more workflow instances can be solved in polynomial time.

PREIMAGE CONSTRUCTION problem by Kratsch and Hemaspaandra naturally arose from the famous graph reconstruction conjecture. It deals with the algorithmic aspects of the conjecture. We present an O(n8) time algorithm for PREIMAGE CONSTRUCTION on permutation graphs and an O(n4(n+m)) time algorithm for PREIMAGE CONSTRUCTION on distance-hereditary graphs, where n is the number of graphs in the input, and m is the number of edges in a preimage. Since each graph of the input has n-1 vertices and O(n2) edges, the input size is O(n3) (, or O(nm)). There are polynomial time isomorphism algorithms for permutation graphs and distance-hereditary graphs. However the number of permutation (distance-hereditary) graphs obtained by adding a vertex to a permutation (distance-hereditary) graph is generally exponentially large. Thus exhaustive checking of these graphs does not achieve any polynomial time algorithm. Therefore reducing the number of preimage candidates is the key point.

The k-edge-connectivity augmentation problem with bipartition constraints (kECABP, for short) is defined by “Given an undirected graph G=(V, E) and a bipartition π = {VB, VW} of V with VB ∩ VW = ∅, find an edge set Ef of minimum cardinality, consisting of edges that connect VB and VW, such that G'=(V, E ∪ Ef) is k-edge-connected.” The problem has applications for security of statistical data stored in a cross tabulated table, and so on. In this paper we propose a fast algorithm for finding an optimal solution to (σ + 1)ECABP in O(|V||E| + |V2|log |V|) time when G is σ-edge-connected (σ > 0), and show that the problem can be solved in linear time if σ ∈ {1, 2}.

In this paper, we propose an algorithm that solves the node-to-node disjoint paths problem in n-burnt pancake graphs in polynomial-order time of n. We also give a proof of its correctness as well as the estimates of time complexity O(n3) and the maximum path length 3n+4. We conducted a computer experiment for n=2 to 100 to measure the average performance of our algorithm. The results show that the average time complexity is O(n3.0) and the maximum path length is 3n+4.

Petri nets with inhibitor arcs are referred to as inhibitor-arc Petri nets. It is shown that modeling capability of inhibitor-arc Petri nets is equivalent to that of Turing machines. The subject of this paper is the legal firing sequence problem (INLFS) for inhibitor-arc Petri nets: given an inhibitor-arc Petri net IN, an initial marking M0 and a firing count vector X, find a firing sequence δ such that its firing starts from M0 and each transition t appears in δ exactly X(t) times as prescribed by X. The paper is the first step of research for time complexity analysis and designing algorithms of INLFS, one of the most fundamental problems for inhibitor-arc Petri nets having more modeling capability than ordinary Peri nets. The recognition version of INLFS, denoted as RINLFS, means a decision problem, asking a "yes" or "no" answer on the existence of a solution δ to INLFS. The main results are the following (1) and (2). (1) Proving (1-1) and (1-2) when the underlying Petri net of IN is an unweighted state machine: (1-1) INLFS can be solved in pseudo-polynomial (O(|X|)) time for IN of non-adjacent type having only one special place called a rivet; (1-2) RINLFS is NP-hard for IN with at least three rivets; (2) Proving that RINLFS for IN whose underlying Petri net is unweighted and forward conflict-free is NP-hard. Heuristic algorithms for solving INLFS are going to be proposed in separate papers.

The 2-vertex-connectivity augmentation problem for specified vertices (2VCA-SV) is defined as follows: Given an undirected graph G=(V,E), a subgraph G0=(V,E') of G, a specified set of vertices S V and a weight function w:E R^+ (nonnegative real numbers), find a set E" E-E' with the minimum total weight, such that G0+E"=(V,E' E") has at least two internally disjoint paths between any pair of vertices in S. In this paper, we propose an O(|V||E|+ |V|2 log |V|) time algorithm 2-ABIS, whose performance ratio is 2 (3, respectively), for 2VCA-SV if G0 has a connected component containing S (otherwise).

The k-vertex-connectivity augmentation problem for a specified set of vertices of a graph with degree-unchangeable vertices, kVCA(G,S,D), is defined as follows: "Given a positive integer k, an undirected graph G=(V,E), a specified set of vertices S V and a set of degree-changeable vertices D V, find a smallest set of edges E such that the vertex-connectivity of S in (V,E E) is at least k and E {(u,v) u,v D}. " The main result of the paper is that checking the existence of a solution and finding a solution to 2VCA(G,S,D) or 3VCA(G,S,D) can be done in O(|V|+|E|) or O(|V|(|V|+|E|)) time, respectively.

The legal firing sequence problem (LFS) asks if it is possible to fire each transition some prescribed number of times in a given Petri net. It is a fundamental problem in Petri net theory as it appears as a subproblem, or as a simplified version of marking reachability, minimum initial resource allocation, liveness, and some scheduling problems. It is also known to be NP-hard, however, even under various restrictions on nets (and on firing counts), and no efficient algorithm has been previously reported for any class of nets having general edge weights. We show in this paper that LFS can be solved in polynomial time (in O(n log n) time) for a subclass of state machines, called cacti, with arbitrary edge weights allowed (if each transition is asked to be fired exactly once).

The subject of the paper is to give an overview and latest results on the Legal Firing Sequence Problem of Petri nets (LFS for short). LFS is very fundamental in the sense that it appears as a subproblem or a simpler form of various basic problems in Petri net theory, such as the well-known marking reachability problem, the minimum initial resource allocation problem, the liveness (of level 4) problem, the scheduling problem and so on. However, solving LFS generally is not easy: it is NP -hard even for Petri nets having very simple structures. This intractability of LFS may have been preventing us from producing efficient algorithms for those problems. So research on LFS from computational complexity point of view seems to be rewarding.