431,615 research outputs found
Cram\'er-Rao bounds for synchronization of rotations
Synchronization of rotations is the problem of estimating a set of rotations
R_i in SO(n), i = 1, ..., N, based on noisy measurements of relative rotations
R_i R_j^T. This fundamental problem has found many recent applications, most
importantly in structural biology. We provide a framework to study
synchronization as estimation on Riemannian manifolds for arbitrary n under a
large family of noise models. The noise models we address encompass zero-mean
isotropic noise, and we develop tools for Gaussian-like as well as heavy-tail
types of noise in particular. As a main contribution, we derive the
Cram\'er-Rao bounds of synchronization, that is, lower-bounds on the variance
of unbiased estimators. We find that these bounds are structured by the
pseudoinverse of the measurement graph Laplacian, where edge weights are
proportional to measurement quality. We leverage this to provide interpretation
in terms of random walks and visualization tools for these bounds in both the
anchored and anchor-free scenarios. Similar bounds previously established were
limited to rotations in the plane and Gaussian-like noise
Compressed sensing reconstruction using Expectation Propagation
Many interesting problems in fields ranging from telecommunications to
computational biology can be formalized in terms of large underdetermined
systems of linear equations with additional constraints or regularizers. One of
the most studied ones, the Compressed Sensing problem (CS), consists in finding
the solution with the smallest number of non-zero components of a given system
of linear equations for known
measurement vector and sensing matrix . Here, we
will address the compressed sensing problem within a Bayesian inference
framework where the sparsity constraint is remapped into a singular prior
distribution (called Spike-and-Slab or Bernoulli-Gauss). Solution to the
problem is attempted through the computation of marginal distributions via
Expectation Propagation (EP), an iterative computational scheme originally
developed in Statistical Physics. We will show that this strategy is
comparatively more accurate than the alternatives in solving instances of CS
generated from statistically correlated measurement matrices. For computational
strategies based on the Bayesian framework such as variants of Belief
Propagation, this is to be expected, as they implicitly rely on the hypothesis
of statistical independence among the entries of the sensing matrix. Perhaps
surprisingly, the method outperforms uniformly also all the other
state-of-the-art methods in our tests.Comment: 20 pages, 6 figure
Time as It Could Be Measured in Artificial Living Systems
Being able to measure time, whether directly or indirectly, is a significant advantage for an organism. It permits it to predict regular events, and prepare for them on time. Thus, clocks are ubiquitous in biology. In the present paper, we consider the most minimal abstract pure clocks and investigate their characteristics with respect to their ability to measure time. Amongst other, we find fundamentally diametral clock characteristics, such as oscillatory behaviour for local time measurement or decay-based clocks measuring time periods in scales global to the problem. We include also cascades of independent clocks (“clock bags”) and composite clocks with controlled dependency; the latter show various regimes of markedly different dynamics.Final Published versio
EFFECTS OF GUIDED DISCOVERY AND PROBLEM-SOLVING INSTRUCTIONAL STRATEGIES ON ACHIEVEMENT AND RETENTION OF BIOLOGY STUDENTS IN DELTA CENTRAL SENATORIAL DISTRICT, NIGERIA
This study investigated the effects of guided discovery and problem-solving instructional strategies on the achievement and retention of biology students in Delta Central Senatorial District of Delta State. Ten research questions and ten research hypotheses guided the study. The study adopted the pre-test post-test control group quasi-experimental research design. A sample size of 238 senior secondary school two (SS2) Biology students from six mixed secondary schools in Delta Central Senatorial District was used for the study. The instrument used for data collection was a biology achievement test (BAT) validated by one Biology science educator, an expert in measurement and evaluation and an experienced biology teacher. The reliability of the instrument was established using Kuder Richardson formula 21 which yielded a coefficient of 0.83. Data were collected by administering the BAT as a pre-test, post-test and follow-up test. The data collected were analyzed using mean, standard deviation, paired and independent sample t-test, ANOVA and ANCOVA. The results showed that there was a significant difference in the mean achievement scores in biology among students in guided discovery, problem-solving instructional strategies and lecture method with students in the guided discovery group scoring the highest mark followed by students in problem-solving and lecture method respectively. The result also revealed that there was a significant difference in the mean retention score among students taught with guided discovery, problem-solving instructional strategies and lecture methods. The result further showed that there was no significant interaction effect between teaching methods and sex on achievement and retention. It was recommended that biology teachers should adopt guided discovery and problem-solving instructional strategies in teaching biology concepts. Special training on how to use these teaching strategies should be organized for biology teachers to help them effectively implement guided discovery and problem-solving instructional strategies in classroom teaching. Article visualizations
Eigenvector Synchronization, Graph Rigidity and the Molecule Problem
The graph realization problem has received a great deal of attention in
recent years, due to its importance in applications such as wireless sensor
networks and structural biology. In this paper, we extend on previous work and
propose the 3D-ASAP algorithm, for the graph realization problem in
, given a sparse and noisy set of distance measurements. 3D-ASAP
is a divide and conquer, non-incremental and non-iterative algorithm, which
integrates local distance information into a global structure determination.
Our approach starts with identifying, for every node, a subgraph of its 1-hop
neighborhood graph, which can be accurately embedded in its own coordinate
system. In the noise-free case, the computed coordinates of the sensors in each
patch must agree with their global positioning up to some unknown rigid motion,
that is, up to translation, rotation and possibly reflection. In other words,
to every patch there corresponds an element of the Euclidean group Euc(3) of
rigid transformations in , and the goal is to estimate the group
elements that will properly align all the patches in a globally consistent way.
Furthermore, 3D-ASAP successfully incorporates information specific to the
molecule problem in structural biology, in particular information on known
substructures and their orientation. In addition, we also propose 3D-SP-ASAP, a
faster version of 3D-ASAP, which uses a spectral partitioning algorithm as a
preprocessing step for dividing the initial graph into smaller subgraphs. Our
extensive numerical simulations show that 3D-ASAP and 3D-SP-ASAP are very
robust to high levels of noise in the measured distances and to sparse
connectivity in the measurement graph, and compare favorably to similar
state-of-the art localization algorithms.Comment: 49 pages, 8 figure
Parameter estimation in kinetic reaction models using nonlinear observers facilitated by model extensions
An essential part of mathematical modelling is the accurate and reliable estimation of model parameters. In biology, the required parameters are particularly difficult to measure due to either shortcomings of the measurement technology or a lack of direct measurements. In both cases, parameters must be estimated from indirect measurements, usually in the form of time-series data. Here, we present a novel approach for parameter estimation that is particularly tailored to biological models consisting of nonlinear ordinary differential equations. By assuming specific types of nonlinearities common in biology, resulting from generalised mass action, Hill kinetics and products thereof, we can take a three step approach: (1) transform the identification into an observer problem using a suitable model extension that decouples the estimation of non-measured states from the parameters; (2) reconstruct all extended states using suitable nonlinear observers; (3) estimate the parameters using the reconstructed states. The actual estimation of the parameters is based on the intrinsic dependencies of the extended states arising from the definitions of the extended variables. An important advantage of the proposed method is that it allows to identify suitable measurements and/or model structures for which the parameters can be estimated. Furthermore, the proposed identification approach is generally applicable to models of metabolic networks, signal transduction and gene regulation
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