3D tumor localization through real-time volumetric x-ray imaging for lung cancer radiotherapy

Recently we have developed an algorithm for reconstructing volumetric images and extracting 3D tumor motion information from a single x-ray projection. We have demonstrated its feasibility using a digital respiratory phantom with regular breathing patterns. In this work, we present a detailed description and a comprehensive evaluation of the improved algorithm. The algorithm was improved by incorporating respiratory motion prediction. The accuracy and efficiency were then evaluated on 1) a digital respiratory phantom, 2) a physical respiratory phantom, and 3) five lung cancer patients. These evaluation cases include both regular and irregular breathing patterns that are different from the training dataset. For the digital respiratory phantom with regular and irregular breathing, the average 3D tumor localization error is less than 1 mm. On an NVIDIA Tesla C1060 GPU card, the average computation time for 3D tumor localization from each projection ranges between 0.19 and 0.26 seconds, for both regular and irregular breathing, which is about a 10% improvement over previously reported results. For the physical respiratory phantom, an average tumor localization error below 1 mm was achieved with an average computation time of 0.13 and 0.16 seconds on the same GPU card, for regular and irregular breathing, respectively. For the five lung cancer patients, the average tumor localization error is below 2 mm in both the axial and tangential directions. The average computation time on the same GPU card ranges between 0.26 and 0.34 seconds

Prediction Properties of Aitken's Iterated Delta^2 Process, of Wynn's Epsilon Algorithm, and of Brezinski's Iterated Theta Algorithm

The prediction properties of Aitken's iterated Delta^2 process, Wynn's epsilon algorithm, and Brezinski's iterated theta algorithm for (formal) power series are analyzed. As a first step, the defining recursive schemes of these transformations are suitably rearranged in order to permit the derivation of accuracy-through-order relationships. On the basis of these relationships, the rational approximants can be rewritten as a partial sum plus an appropriate transformation term. A Taylor expansion of such a transformation term, which is a rational function and which can be computed recursively, produces the predictions for those coefficients of the (formal) power series which were not used for the computation of the corresponding rational approximant.Comment: 34 pages, LaTe

Multiparameter spectral analysis for aeroelastic instability problems

This paper presents a novel application of multiparameter spectral theory to the study of structural stability, with particular emphasis on aeroelastic flutter. Methods of multiparameter analysis allow the development of new solution algorithms for aeroelastic flutter problems; most significantly, a direct solver for polynomial problems of arbitrary order and size, something which has not before been achieved. Two major variants of this direct solver are presented, and their computational characteristics are compared. Both are effective for smaller problems arising in reduced-order modelling and preliminary design optimization. Extensions and improvements to this new conceptual framework and solution method are then discussed.Comment: 20 pages, 8 figure

The Degrees of Freedom of Partial Least Squares Regression

The derivation of statistical properties for Partial Least Squares regression can be a challenging task. The reason is that the construction of latent components from the predictor variables also depends on the response variable. While this typically leads to good performance and interpretable models in practice, it makes the statistical analysis more involved. In this work, we study the intrinsic complexity of Partial Least Squares Regression. Our contribution is an unbiased estimate of its Degrees of Freedom. It is defined as the trace of the first derivative of the fitted values, seen as a function of the response. We establish two equivalent representations that rely on the close connection of Partial Least Squares to matrix decompositions and Krylov subspace techniques. We show that the Degrees of Freedom depend on the collinearity of the predictor variables: The lower the collinearity is, the higher the Degrees of Freedom are. In particular, they are typically higher than the naive approach that defines the Degrees of Freedom as the number of components. Further, we illustrate how the Degrees of Freedom approach can be used for the comparison of different regression methods. In the experimental section, we show that our Degrees of Freedom estimate in combination with information criteria is useful for model selection.Comment: to appear in the Journal of the American Statistical Associatio

Inferring causal relations from multivariate time series : a fast method for large-scale gene expression data

Various multivariate time series analysis techniques have been developed with the aim of inferring causal relations between time series. Previously, these techniques have proved their effectiveness on economic and neurophysiological data, which normally consist of hundreds of samples. However, in their applications to gene regulatory inference, the small sample size of gene expression time series poses an obstacle. In this paper, we describe some of the most commonly used multivariate inference techniques and show the potential challenge related to gene expression analysis. In response, we propose a directed partial correlation (DPC) algorithm as an efficient and effective solution to causal/regulatory relations inference on small sample gene expression data. Comparative evaluations on the existing techniques and the proposed method are presented. To draw reliable conclusions, a comprehensive benchmarking on data sets of various setups is essential. Three experiments are designed to assess these methods in a coherent manner. Detailed analysis of experimental results not only reveals good accuracy of the proposed DPC method in large-scale prediction, but also gives much insight into all methods under evaluation

In-Network Distributed Solar Current Prediction

Long-term sensor network deployments demand careful power management. While managing power requires understanding the amount of energy harvestable from the local environment, current solar prediction methods rely only on recent local history, which makes them susceptible to high variability. In this paper, we present a model and algorithms for distributed solar current prediction, based on multiple linear regression to predict future solar current based on local, in-situ climatic and solar measurements. These algorithms leverage spatial information from neighbors and adapt to the changing local conditions not captured by global climatic information. We implement these algorithms on our Fleck platform and run a 7-week-long experiment validating our work. In analyzing our results from this experiment, we determined that computing our model requires an increased energy expenditure of 4.5mJ over simpler models (on the order of 10^{-7}% of the harvested energy) to gain a prediction improvement of 39.7%.Comment: 28 pages, accepted at TOSN and awaiting publicatio

High Dimensional Classification with combined Adaptive Sparse PLS and Logistic Regression

Motivation: The high dimensionality of genomic data calls for the development of specific classification methodologies, especially to prevent over-optimistic predictions. This challenge can be tackled by compression and variable selection, which combined constitute a powerful framework for classification, as well as data visualization and interpretation. However, current proposed combinations lead to instable and non convergent methods due to inappropriate computational frameworks. We hereby propose a stable and convergent approach for classification in high dimensional based on sparse Partial Least Squares (sparse PLS). Results: We start by proposing a new solution for the sparse PLS problem that is based on proximal operators for the case of univariate responses. Then we develop an adaptive version of the sparse PLS for classification, which combines iterative optimization of logistic regression and sparse PLS to ensure convergence and stability. Our results are confirmed on synthetic and experimental data. In particular we show how crucial convergence and stability can be when cross-validation is involved for calibration purposes. Using gene expression data we explore the prediction of breast cancer relapse. We also propose a multicategorial version of our method on the prediction of cell-types based on single-cell expression data. Availability: Our approach is implemented in the plsgenomics R-package.Comment: 9 pages, 3 figures, 4 tables + Supplementary Materials 8 pages, 3 figures, 10 table