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BackgroundRecent advances in nucleic acid sequencing technologies have led to a dramatic increase in the number of markers available to generate genetic linkage maps. This increased marker density can be used to improve genome assemblies as well as add much needed resolution for loci controlling variation in ecologically and agriculturally important traits. However, traditional genetic map construction methods from these large marker datasets can be computationally prohibitive and highly error prone.ResultsWe present TSPmap, a method which implements both approximate and exact Traveling Salesperson Problem solvers to generate linkage maps. We demonstrate that for datasets with large numbers of genomic markers (e.g. 10,000) and in multiple population types generated from inbred parents, TSPmap can rapidly produce high quality linkage maps with low sensitivity to missing and erroneous genotyping data compared to two other benchmark methods, JoinMap and MSTmap. TSPmap is open source and freely available as an R package.ConclusionsWith the advancement of low cost sequencing technologies, the number of markers used in the generation of genetic maps is expected to continue to rise. TSPmap will be a useful tool to handle such large datasets into the future, quickly producing high quality maps using a large number of genomic markers.

The surface-water hydrographs of rivers exhibit large variations due to many natural phenomena. One of the most commonly used approaches for interpolating and extending streamflow records is to fit observed data with an analytic power model. However, such analytic models may not adequately represent the flow process, because they are based on many simplifying assumptions about the natural phenomena that influence the river flow. This paper demonstrates how a neural network can be used as an adaptive model synthesizer as well as a predictor. Issues such as selecting an appropriate neural network architecture and a correct training algorithm as well as presenting data to neural networks are addressed using a constructive algorithm called the cascade-correlation algorithm. The neural-network approach is applied to the flow prediction of the Huron River at the Dexter sampling station, near Ann Arbor, Mich. Empirical comparisons are performed between the predictive capability of the neural network models and the most commonly used analytic nonlinear power model in terms of accuracy and convenience of use. Our preliminary results are quite encouraging. An analysis performed on the structure of the networks developed by the cascade-correlation algorithm shows that the neural networks are capable of adapting their complexity to match changes in the flow history and that the models developed by the neural-network approach are more complex than the power model.

Generalized Partition Crossover (GPX) is a deterministic recombination operator developed for the Traveling Salesman Problem. Partition crossover operators return the best of 2 k reachable offspring, where k is the number of recombining components. This article introduces a new GPX2 operator, which finds more recombining components than GPX or Iterative Partial Transcription (IPT). We also show that GPX2 has O(n) runtime complexity, while also introducing new enhancements to reduce the execution time of GPX2. Finally, we experimentally demonstrate the efficiency of GPX2 when it is used to improve solutions found by the multitrial Lin-Kernighan-Helsgaum (LKH) algorithm. Significant improvements in performance are documented on large (n > 5000) and very large (n = 100 , 000) instances of the Traveling Salesman Problem. [ABSTRACT FROM AUTHOR]

Enabled by rapid advances in computational sciences, in silico logical modeling of complex and large biological networks is more and more feasible making it an increasingly popular approach among biologists. Automated high-throughput, drug target identification is one of the primary goals of this in silico network biology. Targets identified in this way are then used to mine a library of drug chemical compounds in order to identify appropriate therapies. While identification of drug targets is exhaustively feasible on small networks, it remains computationally difficult on moderate and larger models. Moreover, there are several important constraints such as off-target effects, efficacy and safety that should be integrated into the identification of targets if the intention is translation to the clinical space. Here we introduce numerical constraints whereby efficacy is represented by efficiency in response and robustness of outcome. This paper introduces an algorithm that relies on a Constraint Satisfaction (CS) technique to efficiently compute the Minimal Intervention Sets (MIS) within a set of often complex clinical safety constraints with the aim of identifying the smallest least invasive set of targets pharmacologically accessible for therapy that most efficiently and reliably achieve the desired outcome. [ABSTRACT FROM AUTHOR]

The NK hybrid genetic algorithm (GA) for clustering is proposed in this paper. In order to evaluate the solutions, the hybrid algorithm uses the NK clustering validation criterion 2 (NKCV2). NKCV2 uses information about the disposition of ${N}$ small groups of objects. Each group is composed of ${K+1}$ objects of the dataset. Experimental results show that density-based regions can be identified by using NKCV2 with fixed small ${K}$. In NKCV2, the relationship between decision variables is known, which in turn allows us to apply gray box optimization. Mutation operators, a partition crossover (PX), and a local search strategy are proposed, all using information about the relationship between decision variables. In PX, the evaluation function is decomposed into ${q}$ independent components; PX then deterministically returns the best among ${2^{q}}$ possible offspring with computational complexity ${O(N)}$. The NK hybrid GA allows the detection of clusters with arbitrary shapes and the automatic estimation of the number of clusters. In the experiments, the NK hybrid GA produced very good results when compared to another GA approach and to state-of-art clustering algorithms. [ABSTRACT FROM AUTHOR]

Data anonymization techniques have received extensive attention in the privacy research community over the past several years. Various models of privacy preservation have been proposed: k-anonymity, ℓ-diversity and t-closeness, to name a few. An oft-cited drawback of these models is that there is considerable loss in data quality arising from the use of generalization and suppression techniques. Optimization attempts in this context have so far focused on maximizing the data utility for a pre-specified level of privacy. To determine if better privacy levels are obtainable with the same level of data utility, majority of the existing formulations require exhaustive analysis. Further, the data publisher's perspective is often missed in the process. The publisher wishes to maintain a given level of data utility (since the data utility is the revenue earner) and then maximize the level of privacy within acceptable limits. In this paper, we explore this privacy versus data quality trade-off as a multi-objective optimization problem. Our goal is to provide substantial information to a data publisher about the trade-offs available between the privacy level and the information content of an anonymized data set. [ABSTRACT FROM AUTHOR]

An ultrafast pulse shaper for coherent control applications is described, complete with a simple, reliable calibration technique and an advanced learning control algorithm. The calibration technique makes use of a common-path interferometer, producing less noisy measurements than a conventional Mach–Zehnder interferometer. A covariance matrix adaptation evolutionary strategy (ES) is demonstrated to perform better than a traditional ES for high-dimensional search landscapes. [ABSTRACT FROM AUTHOR]

Representations are formalized as encodings that map the search space to the vertex set of a graph. We define the notion of bit equivalent encodings and show that for such encodings the corresponding Walsh coefficients are also conserved. We focus on Gray codes as particular types of encoding and present a review of properties related to the use of Gray codes. Gray codes are widely used in conjunction with genetic algorithms and bit-climbing algorithms for parameter optimization problems. We present new convergence proofs for a special class of unimodal functions; the proofs show that a steepest ascent bit climber using any reflected Gray code representation reaches the global optimum in a number of steps that is linear with respect to the encoding size. There are in fact many different Gray codes. Shifting is defined as a mechanism for dynamically switching from one Gray code representation to another in order to escape local optima. Theoretical results that substantially improve our understanding of the Gray codes and the shifting mechanism are presented. New proofs also shed light on the number of unique Gray code neighborhoods accessible via shifting and on how neighborhood structure changes during shifting. We show that shifting can improve the performance of both a local search algorithm as well as one of the best genetic algorithms currently available. [ABSTRACT FROM AUTHOR]

Presents theorems establishing the bounds of epistasis for problems that can be stated as mathematical expressions. Encoding of functions for genetic algorithms; Integration of the extraction theorem and polynomial theorem; Application of the theorems; Details on parity laws and argument centering.

Privacy constraints are typically enforced on shared data that contain sensitive personal attributes. However, owing to its adverse effect on the utility of the data, information loss must be minimized while sanitizing the data. Existing methods for this purpose modify the data only to the extent necessary to satisfy the privacy constraints, thereby asserting that the information loss has been minimized. However, given the subjective nature of information loss, it is often difficult to justify such an assertion. In this paper, we propose an interactive procedure to generate a data generalization scheme that optimally meets the preferences of the data publisher. A data publisher guides the sanitization process by specifying aspirations in terms of desired achievement levels in the objectives. A reference direction based methodology is used to investigate neighborhood solutions if the generated scheme is not acceptable. This approach draws its power from the constructive input received from the publisher about the suitability of a solution before finding a new one. [ABSTRACT FROM AUTHOR]

Presents an article on the journal 'Evolutionary Computation.' Major goals for the journal; Impact factor of the journal.

Knowledge of the Hessian matrix at the landscape optimum of a controlled physical observable offers valuable information about the system robustness to control noise. The Hessian can also assist in physical landscape characterization, which is of particular interest in quantum system control experiments. The recently developed landscape theoretical analysis motivated the compilation of an automated method to learn the Hessian matrix about the global optimum without derivative measurements from noisy data. The current study introduces the forced optimal covariance adaptive learning (FOCAL) technique for this purpose. FOCAL relies on the covariance matrix adaptation evolution strategy (CMA-ES) that exploits covariance information amongst the control variables by means of principal component analysis. The FOCAL technique is designed to operate with experimental optimization, generally involving continuous high-dimensional search landscapes (>30) with large Hessian condition numbers (≳104). This paper introduces the theoretical foundations of the inverse relationship between the covariance learned by the evolution strategy and the actual Hessian matrix of the landscape. FOCAL is presented and demonstrated to retrieve the Hessian matrix with high fidelity on both model landscapes and quantum control experiments, which are observed to possess nonseparable, nonquadratic search landscapes. The recovered Hessian forms were corroborated by physical knowledge of the systems. The implications of FOCAL extend beyond the investigated studies to potentially cover other physically motivated multivariate landscapes. [ABSTRACT FROM AUTHOR]

When working in an unfamiliar online environment, it can be helpful to have an observer that can intervene and guide a user toward a desirable outcome while avoiding undesirable outcomes or frustration. The Intervention Problem is deciding when to intervene in order to help a user. The Intervention Problem is similar to, but distinct from, Plan Recognition because the observer must not only recognize the intended goals of a user but also when to intervene to help the user when necessary. We formalize a family of Intervention Problems and show that how these problems can be solved using a combination of Plan Recognition methods and classification algorithms to decide whether to intervene. For our benchmarks, the classification algorithms dominate three recent Plan Recognition approaches. We then generalize these results to Human-Aware Intervention, where the observer must decide in real time whether to intervene human users solving a cognitively engaging puzzle. Using a revised feature set more appropriate to human behavior, we produce a learned model to recognize when a human user is about to trigger an undesirable outcome. We perform a human-subject study to evaluate the Human-Aware Intervention. We find that the revised model also dominates existing Plan Recognition algorithms in predicting Human-Aware Intervention., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2022 Weerawardhana, Whitley and Roberts.)

The in silico study and reverse engineering of regulatory networks has gained in recognition as an insightful tool for the qualitative study of biological mechanisms that underlie a broad range of complex illness. In the creation of reliable network models, the integration of prior mechanistic knowledge with experimentally observed behavior is hampered by the disparate nature and widespread sparsity of such measurements. The former challenges conventional regression-based parameter fitting while the latter leads to large sets of highly variable network models that are equally compliant with the data. In this paper, we propose a bounded Constraint Satisfaction (CS) based model checking framework for parameter set identification that readily accommodates partial records and the exponential complexity of this problem. We introduce specific criteria to describe the biological plausibility of competing multi-valued regulatory networks that satisfy all the constraints and formulate model identification as a multi-objective optimization problem. Optimization is directed at maximizing structural parsimony of the regulatory network by mitigating excessive control action selectivity while also favoring increased state transition efficiency and robustness of the network's dynamic response. The framework's scalability, computational time and validity is demonstrated on several well-established and well-studied biological networks.