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

A comprehensive study of sparse codes on abnormality detection

Sparse representation has been applied successfully in abnormal event detection, in which the baseline is to learn a dictionary accompanied by sparse codes. While much emphasis is put on discriminative dictionary construction, there are no comparative studies of sparse codes regarding abnormality detection. We comprehensively study two types of sparse codes solutions - greedy algorithms and convex L1-norm solutions - and their impact on abnormality detection performance. We also propose our framework of combining sparse codes with different detection methods. Our comparative experiments are carried out from various angles to better understand the applicability of sparse codes, including computation time, reconstruction error, sparsity, detection accuracy, and their performance combining various detection methods. Experiments show that combining OMP codes with maximum coordinate detection could achieve state-of-the-art performance on the UCSD dataset [14].Comment: 7 page

Decoding the Encoding of Functional Brain Networks: an fMRI Classification Comparison of Non-negative Matrix Factorization (NMF), Independent Component Analysis (ICA), and Sparse Coding Algorithms

Brain networks in fMRI are typically identified using spatial independent component analysis (ICA), yet mathematical constraints such as sparse coding and positivity both provide alternate biologically-plausible frameworks for generating brain networks. Non-negative Matrix Factorization (NMF) would suppress negative BOLD signal by enforcing positivity. Spatial sparse coding algorithms ($L1$ Regularized Learning and K-SVD) would impose local specialization and a discouragement of multitasking, where the total observed activity in a single voxel originates from a restricted number of possible brain networks. The assumptions of independence, positivity, and sparsity to encode task-related brain networks are compared; the resulting brain networks for different constraints are used as basis functions to encode the observed functional activity at a given time point. These encodings are decoded using machine learning to compare both the algorithms and their assumptions, using the time series weights to predict whether a subject is viewing a video, listening to an audio cue, or at rest, in 304 fMRI scans from 51 subjects. For classifying cognitive activity, the sparse coding algorithm of $L1$ Regularized Learning consistently outperformed 4 variations of ICA across different numbers of networks and noise levels (p$<$0.001). The NMF algorithms, which suppressed negative BOLD signal, had the poorest accuracy. Within each algorithm, encodings using sparser spatial networks (containing more zero-valued voxels) had higher classification accuracy (p$<$0.001). The success of sparse coding algorithms may suggest that algorithms which enforce sparse coding, discourage multitasking, and promote local specialization may capture better the underlying source processes than those which allow inexhaustible local processes such as ICA

Graph Scaling Cut with L1-Norm for Classification of Hyperspectral Images

In this paper, we propose an L1 normalized graph based dimensionality reduction method for Hyperspectral images, called as L1-Scaling Cut (L1-SC). The underlying idea of this method is to generate the optimal projection matrix by retaining the original distribution of the data. Though L2-norm is generally preferred for computation, it is sensitive to noise and outliers. However, L1-norm is robust to them. Therefore, we obtain the optimal projection matrix by maximizing the ratio of between-class dispersion to within-class dispersion using L1-norm. Furthermore, an iterative algorithm is described to solve the optimization problem. The experimental results of the HSI classification confirm the effectiveness of the proposed L1-SC method on both noisy and noiseless data.Comment: European Signal Processing Conference 201

Target-adaptive CNN-based pansharpening

We recently proposed a convolutional neural network (CNN) for remote sensing image pansharpening obtaining a significant performance gain over the state of the art. In this paper, we explore a number of architectural and training variations to this baseline, achieving further performance gains with a lightweight network which trains very fast. Leveraging on this latter property, we propose a target-adaptive usage modality which ensures a very good performance also in the presence of a mismatch w.r.t. the training set, and even across different sensors. The proposed method, published online as an off-the-shelf software tool, allows users to perform fast and high-quality CNN-based pansharpening of their own target images on general-purpose hardware