An Informational Test for Random Finite Strings.
Ontology highlight
ABSTRACT:
SUBMITTER: Bonnici V
PROVIDER: S-EPMC7512521 | biostudies-literature | 2018 Dec
REPOSITORIES: biostudies-literature
Publications
An Informational Test for Random Finite Strings.
Bonnici Vincenzo V Manca Vincenzo V
Entropy (Basel, Switzerland) 20181206 12
In this paper, by extending some results of informational genomics, we present a new randomness test based on the empirical entropy of strings and some properties of the repeatability and unrepeatability of substrings of certain lengths. We give the theoretical motivations of our method and some experimental results of its application to a wide class of strings: decimal representations of real numbers, roulette outcomes, logistic maps, linear congruential generators, quantum measurements, natura ...[more]
Similar Datasets
Project description:Parameter estimation is one of the key technologies for system identification. The Bayesian parameter estimation algorithms are very important for identifying stochastic systems. In this paper, a random finite set based algorithm is proposed to overcome the disadvantages of the existing Bayesian parameter estimation algorithms. It can estimate the unknown parameters of the stochastic system which consists of a varying number of constituent elements by using the measurements disturbed by false detections, missed detections and noises. The models used for parameter estimation are constructed by using random finite set. Based on the proposed system model and measurement model, the key principles and formula derivation of the proposed algorithm are detailed. Then, the implementation of the algorithm is presented by using sequential Monte Carlo based Probability Hypothesis Density (PHD) filter and simulated tempering based importance sampling. Finally, the experiments of systematic errors estimation of multiple sensors are provided to prove the main advantages of the proposed algorithm. The sensitivity analysis is carried out to further study the mechanism of the algorithm. The experimental results verify the superiority of the proposed algorithm.
| S-EPMC7513093 | biostudies-literature
Project description:A CDKN2A/p16 mutation confers 28%-67% lifetime melanoma risk, a risk that may be moderated by ultraviolet radiation exposure. The aim of this study was to test whether melanoma genetic counseling and test disclosure conferred unique informational, motivational, or emotional benefits compared to family history-based counseling. Participants included were 114 unaffected members of melanoma-prone families, ages 16-69, 51.8% men, 65.8% with minor children or grandchildren. Carriers (n = 28) and noncarriers (n = 41) from families with a CDKN2A mutation were compared to no-test controls (n = 45) from melanoma-prone families without an identifiable CDKN2A mutation. All participants received equivalent counseling about melanoma risk and management; only CDKN2A participants received genetic test results. Using newly developed inventories, participants rated perceived costs and benefits for managing their own and their children's or grandchildren's melanoma risk 1 month and 1 year after counseling. Propensity scores controlled for baseline family differences. Compared to no-test controls, participants who received test results (carriers and noncarriers) reported feeling significantly more informed and prepared to manage their risk, and carriers reported greater motivation to reduce sun exposure. All groups reported low negative emotions about melanoma risk. Parents reported high levels of preparedness to manage children's risk regardless of group. Carrier parents reported greater (but moderate) worry about their children's risk than no-test control parents. Women, older, and more educated respondents reported greater informational and motivational benefits regardless of group. Genetic test results were perceived as more informative and motivating for personal sun protection efforts than equivalent counseling based on family history alone.
| S-EPMC6065541 | biostudies-literature
Project description:Myosin-powered force generation and contraction in nonmuscle cells underlies many cell biological processes and is based on contractility of random actin arrays. This contractility must rely on a microscopic asymmetry, the precise mechanism of which is not completely clear. A number of models of mechanical and structural asymmetries in actomyosin contraction have been posited. Here, we examine a contraction mechanism based on a finite size of myosin clusters and anisotropy of force generation by myosin heads at the ends of the myosin clusters. We use agent-based numerical simulations to demonstrate that if average lengths of actin filaments and myosin clusters are similar, then the proposed microscopic asymmetry leads to effective contraction of random 1D actomyosin arrays. We discuss the model's implication for mechanics of contractile rings and stress fibers.
| S-EPMC5567592 | biostudies-literature
Project description:An optimal clinical specimen for accurate detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) by minimizing the usage of consumables and reduce hazard exposure to healthcare workers is an urgent priority. The diagnostic performance of SARS-CoV-2 detection between healthcare worker-collected nasopharyngeal and oropharyngeal (NP + OP) swabs and patient performed self-collected random saliva was assessed. Paired NP + OP swabs and random saliva were collected and processed within 48 h of specimen collection from two cohort studies which recruited 562 asymptomatic adult candidates. Real-time reverse-transcription polymerase chain reaction targeting Open reading frame 1a (ORF1a) and nucleocapsid (N) genes was performed and the results were compared. Overall, 65 of 562 (28.1%) candidates tested positive for COVID-19 based on random saliva, NP + OP swabs, or both testing techniques. The detection rate of SARS-CoV-2 was higher in random saliva compared to NP + OP testing (92.3%; 60/65 vs. 73.8%; 48/65; p < .05). The estimated sensitivity and specificity of random saliva were higher than NP + OP swabs (95.0; 99.9 vs. 72.2; 99.4). The Ct values of ORF1a and N genes were significantly lower in random saliva compared to NP + OP swabs specimens. Our findings demonstrate that random saliva is an alternative diagnostic specimen for the detection of SARS-CoV-2. Self-collected random oropharyngeal saliva is a valuable specimen that provides accurate SARS-CoV-2 surveillance testing of a community.
| S-EPMC7986796 | biostudies-literature
Project description:Many sociological theories make critically different macropredictions when their microassumptions are implemented stochastically rather than deterministically. Deviations from individuals' behavioral patterns described by microtheories can spark cascades that change macrooutcomes, even when deviations are rare and random. With two experiments, we empirically tested whether macrophenomena can be critically shaped by random deviations. Ninety-six percent of participants' decisions were in line with a deterministic theory of bounded rationality. Despite this impressive microlevel accuracy, the deterministic model failed to predict the observed macrooutcomes. However, a stochastic version of the same microtheory largely improved macropredictions. The stochastic model also correctly predicted the conditions under which deviations mattered. Results also supported the hypothesis that nonrandom deviations can result in fundamentally different macrooutcomes than random deviations. In conclusion, we echo the warning that deterministic microtheories can be misleading. Our findings show that taking into account deviations in sociological theories can improve explanations and predictions.
| S-EPMC7324148 | biostudies-literature
Project description:Video-based pre-test information is used in high resource settings to increase HIV testing coverage but remains untested in resource-limited settings. We conducted formative and evaluative focus group discussions with healthcare workers (HCWs) and caregivers of children in Kenya to develop and refine a pediatric HIV pre-test informational video. We then assessed HIV knowledge among caregivers sequentially enrolled in one of three pre-test information groups: (1) individual HCW-led (N = 50), (2) individual video-based (N = 50), and (3) group video-based (N = 50) sessions. A brief video incorporating information on national pediatric testing, modes of HIV transmission, and dramatized testimonials of caregivers who tested children was produced in three languages. Compared to individual HCW-led sessions (mean: 7.2/9; standard deviation [SD]: 1.3), both the group video-based (mean: 7.7; SD: 0.9) and individual video-based (mean: 7.6; SD: 0.9) sessions had higher mean knowledge scores. Video-based pre-test information could enhance existing pediatric HIV testing services.
| S-EPMC9176162 | biostudies-literature
Project description:BackgroundThe center string (or closest string) problem is a classic computer science problem with important applications in computational biology. Given k input strings and a distance threshold d, we search for a string within Hamming distance at most d to each input string. This problem is NP complete.ResultsIn this paper, we focus on exact methods for the problem that are also swift in application. We first introduce data reduction techniques that allow us to infer that certain instances have no solution, or that a center string must satisfy certain conditions. We describe how to use this information to speed up two previously published search tree algorithms. Then, we describe a novel iterative search strategy that is efficient in practice, where some of our reduction techniques can also be applied. Finally, we present results of an evaluation study for two different data sets from a biological application.ConclusionsWe find that the running time for computing the optimal center string is dominated by the subroutine calls for d = dopt -1 and d = dopt. Our data reduction is very effective for both, either rejecting unsolvable instances or solving trivial positions. We find that this speeds up computations considerably.
| S-EPMC3108310 | biostudies-literature
Project description:The relative merits of cooperation and self-interest in an ensemble of strategic interactions can be investigated by using finite random games. In finite random games, finitely many players have finite numbers of actions and independently and identically distributed (iid) random payoffs with continuous distribution functions. In each realization, players are shown the values of all payoffs and then choose their strategies simultaneously. Noncooperative self-interest is modeled by Nash equilibrium (NE). Cooperation is advantageous when a NE is Pareto-inefficient. In ordinal games, the numerical value of the payoff function gives each player's ordinal ranking of payoffs. For a fixed number of players, as the number of actions of any player increases, the conditional probability that a pure strategic profile is not pure Pareto-optimal, given that it is a pure NE, apparently increases, but is bounded above strictly below 1. In games with transferable utility, the numerical payoff values may be averaged across actions (so that mixed NEs are meaningful) and added across players. In simulations of two-player games when both players have small, equal numbers of actions, as the number of actions increases, the probability that a NE (pure and mixed) attains the cooperative maximum declines rapidly; the gain from cooperation relative to the Nash high value decreases; and the gain from cooperation relative to the Nash low value rises dramatically. In the cases studied here, with an increasing number of actions, cooperation is increasingly likely to become advantageous compared with pure self-interest, but self-interest can achieve all that cooperation could achieve in a nonnegligible fraction of cases. These results can be interpreted in terms of cooperation in societies and mutualism in biology.
| S-EPMC21404 | biostudies-other
Project description:Many real datasets contain values missing not at random (MNAR). In this scenario, investigators often perform list-wise deletion, or delete samples with any missing values, before applying causal discovery algorithms. List-wise deletion is a sound and general strategy when paired with algorithms such as FCI and RFCI, but the deletion procedure also eliminates otherwise good samples that contain only a few missing values. In this report, we show that we can more efficiently utilize the observed values with test-wise deletion while still maintaining algorithmic soundness. Here, test-wise deletion refers to the process of list-wise deleting samples only among the variables required for each conditional independence (CI) test used in constraint-based searches. Test-wise deletion therefore often saves more samples than list-wise deletion for each CI test, especially when we have a sparse underlying graph. Our theoretical results show that test-wise deletion is sound under the justifiable assumption that none of the missingness mechanisms causally affect each other in the underlying causal graph. We also find that FCI and RFCI with test-wise deletion outperform their list-wise deletion and imputation counterparts on average when MNAR holds in both synthetic and real data.
| S-EPMC6638553 | biostudies-literature
Project description:Testing for random mating of a population is important in population genetics, because deviations from randomness of mating may indicate inbreeding, population stratification, natural selection, or sampling bias. However, current methods use only observed numbers of genotypes and alleles, and do not take advantage of the fact that the advent of sequencing technology provides an opportunity to investigate this topic in unprecedented detail. To address this opportunity, a novel statistical test for random mating is required in population genomics studies for which large sequencing datasets are generally available. Here, we propose a Monte-Carlo-based-permutation test (MCP) as an approach to detect random mating. Computer simulations used to evaluate the performance of the permutation test indicate that its type I error is well controlled and that its statistical power is greater than that of the commonly used chi-square test (CHI). Our simulation study shows the power of our test is greater for datasets characterized by lower levels of migration between subpopulations. In addition, test power increases with increasing recombination rate, sample size, and divergence time of subpopulations. For populations exhibiting limited migration and having average levels of population divergence, the statistical power approaches 1 for sequences longer than 1 Mbp and for samples of 400 individuals or more. Taken together, our results suggest that our permutation test is a valuable tool to detect random mating of populations, especially in population genomics studies.
| S-EPMC3734302 | biostudies-literature