On the Complexity of Exact Pattern Matching in Graphs: Binary Strings and Bounded Degree

Exact pattern matching in labeled graphs is the problem of searching paths of a graph $G=(V,E)$ that spell the same string as the pattern $P[1..m]$. This basic problem can be found at the heart of more complex operations on variation graphs in computational biology, of query operations in graph databases, and of analysis operations in heterogeneous networks, where the nodes of some paths must match a sequence of labels or types. We describe a simple conditional lower bound that, for any constant $\epsilon>0$, an $O(|E|^{1 - \epsilon} \, m)$-time or an $O(|E| \, m^{1 - \epsilon})$-time algorithm for exact pattern matching on graphs, with node labels and patterns drawn from a binary alphabet, cannot be achieved unless the Strong Exponential Time Hypothesis (SETH) is false. The result holds even if restricted to undirected graphs of maximum degree three or directed acyclic graphs of maximum sum of indegree and outdegree three. Although a conditional lower bound of this kind can be somehow derived from previous results (Backurs and Indyk, FOCS'16), we give a direct reduction from SETH for dissemination purposes, as the result might interest researchers from several areas, such as computational biology, graph database, and graph mining, as mentioned before. Indeed, as approximate pattern matching on graphs can be solved in $O(|E|\,m)$ time, exact and approximate matching are thus equally hard (quadratic time) on graphs under the SETH assumption. In comparison, the same problems restricted to strings have linear time vs quadratic time solutions, respectively, where the latter ones have a matching SETH lower bound on computing the edit distance of two strings (Backurs and Indyk, STOC'15).Comment: Using Lemma 12 and Lemma 13 might to be enough to prove Lemma 14. However, the proof of Lemma 14 is correct if you assume that the graph used in the reduction is a DAG. Hence, since the problem is already quadratic for a DAG and a binary alphabet, it has to be quadratic also for a general graph and a binary alphabe

Applications of Bee Colony Optimization

Many computationally difficult problems are attacked using non-exact algorithms, such as approximation algorithms and heuristics. This thesis investigates an ex- ample of the latter, Bee Colony Optimization, on both an established optimization problem in the form of the Quadratic Assignment Problem and the FireFighting problem, which has not been studied before as an optimization problem. Bee Colony Optimization is a swarm intelligence algorithm, a paradigm that has increased in popularity in recent years, and many of these algorithms are based on natural pro- cesses. We tested the Bee Colony Optimization algorithm on the QAPLIB library of Quadratic Assignment Problem instances, which have either optimal or best known solutions readily available, and enabled us to compare the quality of solutions found by the algorithm. In addition, we implemented a couple of other well known algorithms for the Quadratic Assignment Problem and consequently we could analyse the runtime of our algorithm. We introduce the Bee Colony Optimization algorithm for the FireFighting problem. We also implement some greedy algorithms and an Ant Colony Optimization al- gorithm for the FireFighting problem, and compare the results obtained on some randomly generated instances. We conclude that Bee Colony Optimization finds good solutions for the Quadratic Assignment Problem, however further investigation on speedup methods is needed to improve its performance to that of other algorithms. In addition, Bee Colony Optimization is effective on small instances of the FireFighting problem, however as instance size increases the results worsen in comparison to the greedy algorithms, and more work is needed to improve the decisions made on these instances

Separations in Query Complexity Based on Pointer Functions

In 1986, Saks and Wigderson conjectured that the largest separation between deterministic and zero-error randomized query complexity for a total boolean function is given by the function $f$ on $n=2^k$ bits defined by a complete binary tree of NAND gates of depth $k$, which achieves $R_0(f) = O(D(f)^{0.7537\ldots})$. We show this is false by giving an example of a total boolean function $f$ on $n$ bits whose deterministic query complexity is $\Omega(n/\log(n))$ while its zero-error randomized query complexity is $\tilde O(\sqrt{n})$. We further show that the quantum query complexity of the same function is $\tilde O(n^{1/4})$, giving the first example of a total function with a super-quadratic gap between its quantum and deterministic query complexities. We also construct a total boolean function $g$ on $n$ variables that has zero-error randomized query complexity $\Omega(n/\log(n))$ and bounded-error randomized query complexity $R(g) = \tilde O(\sqrt{n})$. This is the first super-linear separation between these two complexity measures. The exact quantum query complexity of the same function is $Q_E(g) = \tilde O(\sqrt{n})$. These two functions show that the relations $D(f) = O(R_1(f)^2)$ and $R_0(f) = \tilde O(R(f)^2)$ are optimal, up to poly-logarithmic factors. Further variations of these functions give additional separations between other query complexity measures: a cubic separation between $Q$ and $R_0$, a $3/2$-power separation between $Q_E$ and $R$, and a 4th power separation between approximate degree and bounded-error randomized query complexity. All of these examples are variants of a function recently introduced by \goos, Pitassi, and Watson which they used to separate the unambiguous 1-certificate complexity from deterministic query complexity and to resolve the famous Clique versus Independent Set problem in communication complexity.Comment: 25 pages, 6 figures. Version 3 improves separation between Q_E and R_0 and updates reference