Behavioral Learning of Aircraft Landing Sequencing Using a Society of Probabilistic Finite State Machines

Air Traffic Control (ATC) is a complex safety critical environment. A tower controller would be making many decisions in real-time to sequence aircraft. While some optimization tools exist to help the controller in some airports, even in these situations, the real sequence of the aircraft adopted by the controller is significantly different from the one proposed by the optimization algorithm. This is due to the very dynamic nature of the environment. The objective of this paper is to test the hypothesis that one can learn from the sequence adopted by the controller some strategies that can act as heuristics in decision support tools for aircraft sequencing. This aim is tested in this paper by attempting to learn sequences generated from a well-known sequencing method that is being used in the real world. The approach relies on a genetic algorithm (GA) to learn these sequences using a society Probabilistic Finite-state Machines (PFSMs). Each PFSM learns a different sub-space; thus, decomposing the learning problem into a group of agents that need to work together to learn the overall problem. Three sequence metrics (Levenshtein, Hamming and Position distances) are compared as the fitness functions in GA. As the results suggest, it is possible to learn the behavior of the algorithm/heuristic that generated the original sequence from very limited information

Partitioning networks into cliques: a randomized heuristic approach

In the context of community detection in social networks, the term community can be grounded in the strict way that simply everybody should know each other within the community. We consider the corresponding community detection problem. We search for a partitioning of a network into the minimum number of non-overlapping cliques, such that the cliques cover all vertices. This problem is called the clique covering problem (CCP) and is one of the classical NP-hard problems. For CCP, we propose a randomized heuristic approach. To construct a high quality solution to CCP, we present an iterated greedy (IG) algorithm. IG can also be combined with a heuristic used to determine how far the algorithm is from the optimum in the worst case. Randomized local search (RLS) for maximum independent set was proposed to find such a bound. The experimental results of IG and the bounds obtained by RLS indicate that IG is a very suitable technique for solving CCP in real-world graphs. In addition, we summarize our basic rigorous results, which were developed for analysis of IG and understanding of its behavior on several relevant graph classes

Kernels of Mallows Models under the Hamming Distance for solving the Quadratic Assignment Problem

The Quadratic Assignment Problem (QAP) is a well-known permutation-based combinatorial optimization problem with real applications in industrial and logistics environments. Motivated by the challenge that this NP-hard problem represents, it has captured the attention of the optimization community for decades. As a result, a large number of algorithms have been proposed to tackle this problem. Among these, exact methods are only able to solve instances of size $n<40$. To overcome this limitation, many metaheuristic methods have been applied to the QAP. In this work, we follow this direction by approaching the QAP through Estimation of Distribution Algorithms (EDAs). Particularly, a non-parametric distance-based exponential probabilistic model is used. Based on the analysis of the characteristics of the QAP, and previous work in the area, we introduce Kernels of Mallows Model under the Hamming distance to the context of EDAs. Conducted experiments point out that the performance of the proposed algorithm in the QAP is superior to (i) the classical EDAs adapted to deal with the QAP, and also (ii) to the specific EDAs proposed in the literature to deal with permutation problems.Severo Ochoa SEV-2013-0323 TIN2016-78365-R PID2019-106453GAI00 SVP-2014-068574 TIN2017-82626-

Common DNA sequence variation influences 3-dimensional conformation of the human genome.

BACKGROUND:The 3-dimensional (3D) conformation of chromatin inside the nucleus is integral to a variety of nuclear processes including transcriptional regulation, DNA replication, and DNA damage repair. Aberrations in 3D chromatin conformation have been implicated in developmental abnormalities and cancer. Despite the importance of 3D chromatin conformation to cellular function and human health, little is known about how 3D chromatin conformation varies in the human population, or whether DNA sequence variation between individuals influences 3D chromatin conformation. RESULTS:To address these questions, we perform Hi-C on lymphoblastoid cell lines from 20 individuals. We identify thousands of regions across the genome where 3D chromatin conformation varies between individuals and find that this variation is often accompanied by variation in gene expression, histone modifications, and transcription factor binding. Moreover, we find that DNA sequence variation influences several features of 3D chromatin conformation including loop strength, contact insulation, contact directionality, and density of local cis contacts. We map hundreds of quantitative trait loci associated with 3D chromatin features and find evidence that some of these same variants are associated at modest levels with other molecular phenotypes as well as complex disease risk. CONCLUSION:Our results demonstrate that common DNA sequence variants can influence 3D chromatin conformation, pointing to a more pervasive role for 3D chromatin conformation in human phenotypic variation than previously recognized

A principal component analysis of 39 scientific impact measures

The impact of scientific publications has traditionally been expressed in terms of citation counts. However, scientific activity has moved online over the past decade. To better capture scientific impact in the digital era, a variety of new impact measures has been proposed on the basis of social network analysis and usage log data. Here we investigate how these new measures relate to each other, and how accurately and completely they express scientific impact. We performed a principal component analysis of the rankings produced by 39 existing and proposed measures of scholarly impact that were calculated on the basis of both citation and usage log data. Our results indicate that the notion of scientific impact is a multi-dimensional construct that can not be adequately measured by any single indicator, although some measures are more suitable than others. The commonly used citation Impact Factor is not positioned at the core of this construct, but at its periphery, and should thus be used with caution

CSM429: Abstract Geometric Crossover for the Permutation Representation

Abstract crossover and abstract mutation are representation-independent operators that are well-defined once a notion of distance over the solution space is defined. They were obtained as generalization of genetic operators for binary strings and real vectors. In this paper we explore how the abstract geometric framework applies to the permutation representation. This representation is challenging for various reasons: because of the inherent difference between permutations and the representations that inspired the abstraction; because the whole notion of geometry over permutation spaces radically departs from traditional geometries and it is almost unexplored mathematical territory; because the many notions of distance available and their subtle interconnections make it hard to see the right distance to use, if any; because the various available interpretations of permutations make ambiguous what a permutation represents, hence, how to treat it; because of the existence of various permutation-like representations that are incorrectly confused with permutations; and finally because of the existence of many mutation and recombination operators and their many variations for the same representation. This article shows that the application of our geometric framework naturally clarifies and unifies an important domain,the permutation representation and the related operators, in which there was little or no hope to find order. In addition the abstract geometric framework is used to improve the design of crossover operators for well-known problems naturally connected with the permutation representation