2,176 research outputs found
Traction force microscopy with optimized regularization and automated Bayesian parameter selection for comparing cells
Adherent cells exert traction forces on to their environment, which allows
them to migrate, to maintain tissue integrity, and to form complex
multicellular structures. This traction can be measured in a perturbation-free
manner with traction force microscopy (TFM). In TFM, traction is usually
calculated via the solution of a linear system, which is complicated by
undersampled input data, acquisition noise, and large condition numbers for
some methods. Therefore, standard TFM algorithms either employ data filtering
or regularization. However, these approaches require a manual selection of
filter- or regularization parameters and consequently exhibit a substantial
degree of subjectiveness. This shortcoming is particularly serious when cells
in different conditions are to be compared because optimal noise suppression
needs to be adapted for every situation, which invariably results in systematic
errors. Here, we systematically test the performance of new methods from
computer vision and Bayesian inference for solving the inverse problem in TFM.
We compare two classical schemes, L1- and L2-regularization, with three
previously untested schemes, namely Elastic Net regularization, Proximal
Gradient Lasso, and Proximal Gradient Elastic Net. Overall, we find that
Elastic Net regularization, which combines L1 and L2 regularization,
outperforms all other methods with regard to accuracy of traction
reconstruction. Next, we develop two methods, Bayesian L2 regularization and
Advanced Bayesian L2 regularization, for automatic, optimal L2 regularization.
Using artificial data and experimental data, we show that these methods enable
robust reconstruction of traction without requiring a difficult selection of
regularization parameters specifically for each data set. Thus, Bayesian
methods can mitigate the considerable uncertainty inherent in comparing
cellular traction forces
The composite absolute penalties family for grouped and hierarchical variable selection
Extracting useful information from high-dimensional data is an important
focus of today's statistical research and practice. Penalized loss function
minimization has been shown to be effective for this task both theoretically
and empirically. With the virtues of both regularization and sparsity, the
-penalized squared error minimization method Lasso has been popular in
regression models and beyond. In this paper, we combine different norms
including to form an intelligent penalty in order to add side information
to the fitting of a regression or classification model to obtain reasonable
estimates. Specifically, we introduce the Composite Absolute Penalties (CAP)
family, which allows given grouping and hierarchical relationships between the
predictors to be expressed. CAP penalties are built by defining groups and
combining the properties of norm penalties at the across-group and within-group
levels. Grouped selection occurs for nonoverlapping groups. Hierarchical
variable selection is reached by defining groups with particular overlapping
patterns. We propose using the BLASSO and cross-validation to compute CAP
estimates in general. For a subfamily of CAP estimates involving only the
and norms, we introduce the iCAP algorithm to trace the entire
regularization path for the grouped selection problem. Within this subfamily,
unbiased estimates of the degrees of freedom (df) are derived so that the
regularization parameter is selected without cross-validation. CAP is shown to
improve on the predictive performance of the LASSO in a series of simulated
experiments, including cases with and possibly mis-specified
groupings. When the complexity of a model is properly calculated, iCAP is seen
to be parsimonious in the experiments.Comment: Published in at http://dx.doi.org/10.1214/07-AOS584 the Annals of
Statistics (http://www.imstat.org/aos/) by the Institute of Mathematical
Statistics (http://www.imstat.org
Continuous-variable quantum neural networks
We introduce a general method for building neural networks on quantum
computers. The quantum neural network is a variational quantum circuit built in
the continuous-variable (CV) architecture, which encodes quantum information in
continuous degrees of freedom such as the amplitudes of the electromagnetic
field. This circuit contains a layered structure of continuously parameterized
gates which is universal for CV quantum computation. Affine transformations and
nonlinear activation functions, two key elements in neural networks, are
enacted in the quantum network using Gaussian and non-Gaussian gates,
respectively. The non-Gaussian gates provide both the nonlinearity and the
universality of the model. Due to the structure of the CV model, the CV quantum
neural network can encode highly nonlinear transformations while remaining
completely unitary. We show how a classical network can be embedded into the
quantum formalism and propose quantum versions of various specialized model
such as convolutional, recurrent, and residual networks. Finally, we present
numerous modeling experiments built with the Strawberry Fields software
library. These experiments, including a classifier for fraud detection, a
network which generates Tetris images, and a hybrid classical-quantum
autoencoder, demonstrate the capability and adaptability of CV quantum neural
networks
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