A new 1.375-approximation algorithm for sorting by transpositions

Background sorting by transpositions (SBT) is a classical problem in genome rearrangements. In 2012, SBT was proven to be $$\mathcal {NP}$$ NP -hard and the best approximation algorithm with a 1.375 ratio was proposed in 2006 by Elias and Hartman (EH algorithm). Their algorithm employs simplification, a technique used to transform an input permutation $$\pi$$ π into a simple permutation$${\hat{\pi }}$$ π ^ , presumably easier to handle with. The permutation $${\hat{\pi }}$$ π ^ is obtained by inserting new symbols into $$\pi$$ π in a way that the lower bound of the transposition distance of $$\pi$$ π is kept on $${\hat{\pi }}$$ π ^ . The simplification is guaranteed to keep the lower bound, not the transposition distance. A sequence of operations sorting $${\hat{\pi }}$$ π ^ can be mimicked to sort $$\pi$$ π . Results and conclusions First, using an algebraic approach, we propose a new upper bound for the transposition distance, which holds for all $$S_n$$ S n . Next, motivated by a problem identified in the EH algorithm, which causes it, in scenarios involving how the input permutation is simplified, to require one extra transposition above the 1.375-approximation ratio, we propose a new approximation algorithm to solve SBT ensuring the 1.375-approximation ratio for all $$S_n$$ S n . We implemented our algorithm and EH’s. Regarding the implementation of the EH algorithm, two other issues were identified and needed to be fixed. We tested both algorithms against all permutations of size n, $$2\le n \le 12$$ 2 ≤ n ≤ 12 . The results show that the EH algorithm exceeds the approximation ratio of 1.375 for permutations with a size greater than 7. The percentage of computed distances that are equal to transposition distance, computed by the implemented algorithms are also compared with others available in the literature. Finally, we investigate the performance of both implementations on longer permutations of maximum length 500. From the experiments, we conclude that maximum and the average distances computed by our algorithm are a little better than the ones computed by the EH algorithm and the running times of both algorithms are similar, despite the time complexity of our algorithm being higher.

An Algebraic Approach to Clustering and Classification with Support Vector Machines

In this note, we propose a novel classification approach by introducing a new clustering method, which is used as an intermediate step to discover the structure of a data set. The proposed clustering algorithm uses similarities and the concept of a clique to obtain clusters, which can be used with different strategies for classification. This approach also reduces the size of the training data set. In this study, we apply support vector machines (SVMs) after obtaining clusters with the proposed clustering algorithm. The proposed clustering algorithm is applied with different strategies for applying SVMs. The results for several real data sets show that the performance is comparable with the standard SVM while reducing the size of the training data set and also the number of support vectors.

The Complexity of Promise SAT on Non-Boolean Domains

While 3-SAT is NP-hard, 2-SAT is solvable in polynomial time. Austrin et al. [SICOMP’17] proved a result known as “(2+ɛ)-SAT is NP-hard.” They showed that the problem of distinguishing k -CNF formulas that are g -satisfiable (i.e., some assignment satisfies at least g literals in every clause) from those that are not even 1-satisfiable is NP-hard if g/k < 1/2 and is in P otherwise. We study a generalisation of SAT on arbitrary finite domains, with clauses that are disjunctions of unary constraints, and establish analogous behaviour. Thus, we give a dichotomy for a natural fragment of promise constraint satisfaction problems ( PCSPs ) on arbitrary finite domains. The hardness side is proved using the algebraic approach via a new general NP-hardness criterion on polymorphisms, which is based on a gap version of the Layered Label Cover problem. We show that previously used criteria are insufficient—the problem hence gives an interesting benchmark of algebraic techniques for proving hardness of approximation in problems such as PCSPs.

A Perspective on "CCS Expressions, Finite State Processes, and Three Problems of Equivalence"

With the publication of the Kannellakis-Smolka 1983 PODC paper, Kanellakis and Smolka pioneered the development of efficient algorithms for deciding behavioral equivalence of concurrent and distributed processes, especially bisimulation equivalence. Bisimulation is the cornerstone of the process-algebraic approach to modeling and verifying concurrent and distributed systems. They also presented complexity results that showed certain behavioral equivalences are computationally intractable. Collectively, their results founded the subdiscipline of algorithmic process theory, and established the associated bridges between the European research community, whose focus at the time was on process theory, and that of the US, with a rich tradition in algorithm design and computational complexity, but to whom process theory was largely unknown.

Finite-Time Trajectory Tracking of Second-Order Systems Using Acceleration Feedback Only

In this paper, an algebraic approach for the finite-time feedback control problem is provided for second-order systems where only the second-order derivative of the controlled variable is measured. In practice, it means that the acceleration is the only variable that can be used for feedback purposes. This problem appears in many mechanical systems such as positioning systems and force-position controllers in robotic systems and aerospace applications. Based on an algebraic approach, an on-line algebraic estimator is developed in order to estimate in finite time the unmeasured position and velocity variables. The obtained expressions depend solely on iterated integrals of the measured acceleration output and of the control input. The approach is shown to be robust to noisy measurements and it has the advantage to provide on-line finite-time (or non-asymptotic) state estimations. Based on these estimations, a quasi-homogeneous second-order sliding mode tracking control law including estimated position error integrals is designed illustrating the possibilities of finite-time acceleration feedback via algebraic state estimation.

Counting Induced Subgraphs: An Algebraic Approach to #W[1]-Hardness

We study the problem $$\#\textsc {IndSub}(\varPhi )$$ # I N D S U B ( Φ ) of counting all induced subgraphs of size k in a graph G that satisfy the property $$\varPhi $$ Φ . It is shown that, given any graph property $$\varPhi $$ Φ that distinguishes independent sets from bicliques, $$\#\textsc {IndSub}(\varPhi )$$ # I N D S U B ( Φ ) is hard for the class $$\#\mathsf {W[1]}$$ # W [ 1 ] , i.e., the parameterized counting equivalent of $${{\mathsf {N}}}{{\mathsf {P}}}$$ N P . Under additional suitable density conditions on $$\varPhi $$ Φ , satisfied e.g. by non-trivial monotone properties on bipartite graphs, we strengthen $$\#\mathsf {W[1]}$$ # W [ 1 ] -hardness by establishing that $$\#\textsc {IndSub}(\varPhi )$$ # I N D S U B ( Φ ) cannot be solved in time $$f(k)\cdot n^{o(k)}$$ f ( k ) · n o ( k ) for any computable function f, unless the Exponential Time Hypothesis fails. Finally, we observe that our results remain true even if the input graph G is restricted to be bipartite and counting is done modulo a fixed prime.

Prestress behaviour and ductility requirements in structures: solutions from a unified algebraic approach

This paper presents an algebraic approach that unifies both the elastic and limit theories of static structural analysis. This approach reveals several previously unpublished improvements, which are based on several dualities in the mathematical description. Firstly, we show a novel duality between the solutions to two different problems: the elastic solution to the internal forces of an externally loaded structure, and the nodal displacements induced by prestressing in one or several elements of the same structure. This duality is proven and discussed. The application of this solution to the limit state analysis is very productive, and includes the determination of the ductility requirements necessary to achieve full plastic behaviour, and the assessment of the prestress needed to limit or eliminate such requirements. The unified framework also allows to obtain the elasto-plastic deformed state at the beginning of the plastic structural collapse. We have also detailed the theoretical duality between two classes of structures—hyperstatic and hypostatic—which was derived from the linear algebra principles that define these solutions. Finally, we studied and exposed the dimensionality reduction of structural problems given by the singular value decomposition and the eigenvalues problem. An illustrative example that clearly illustrates all these points is provided.

The classical limit of Schrödinger operators in the framework of Berezin quantization and spontaneous symmetry breaking as an emergent phenomenon

The algebraic properties of a strict deformation quantization are analyzed on the classical phase space [Formula: see text]. The corresponding quantization maps enable us to take the limit for [Formula: see text] of a suitable sequence of algebraic vector states induced by [Formula: see text]-dependent eigenvectors of several quantum models, in which the sequence converges to a probability measure on [Formula: see text], defining a classical algebraic state. The observables are here represented in terms of a Berezin quantization map which associates classical observables (functions on the phase space) to quantum observables (elements of [Formula: see text] algebras) parametrized by [Formula: see text]. The existence of this classical limit is in particular proved for ground states of a wide class of Schrödinger operators, where the classical limiting state is obtained in terms of a Haar integral. The support of the classical state (a probability measure on the phase space) is included in certain orbits in [Formula: see text] depending on the symmetry of the potential. In addition, since this [Formula: see text]-algebraic approach allows for both quantum and classical theories, it is highly suitable to study the theoretical concept of spontaneous symmetry breaking (SSB) as an emergent phenomenon when passing from the quantum realm to the classical world by switching off [Formula: see text]. To this end, a detailed mathematical description is outlined and it is shown how this algebraic approach sheds new light on spontaneous symmetry breaking in several physical models.