arXiv subjects

James Murphy

Publications and source records attributed to James Murphy.

8 recordsLinked to original sources

arXiv2022

Assessment of fiducial motion in CBCT projections of the abdominal tumor using template matching and sequential stereo triangulation

Purpose: To assess the fiducial motion in abdominal stereotactic body radiotherapy (SBRT) using the cone-beam computed tomography (CBCT) projections acquired for pre-treatment patient set-up. Materials and Methods: Pre-treatment CBCT projections and anterior-posterior (AP) and lateral (LAT) pair of fluoroscopic sequences of 7 pancreatic and 6 liver SBRT patients with implanted fiducials were analyzed for 49 treatment fractions retrospectively. A tracking algorithm based on template matching and sequential stereo triangulation algorithms was used to track the fiducials in the CBCT projections and the fluoro sequence pairs. We predicted the clinical couch adjustment from CBCT tracking and compared it with the clinical couch decision made during the patient's treatment. Results: In 3D coordinate, the fiducial motion ranges for pancreas cases were 9.90+/-3.52 mm, 10.65+/-5.91 mm, and 10.74+/-6.24 mm for CBCT, AP, and LAT fluoro, respectively, while in the liver, they were 13.93+/-3.39 mm, 11.17+/-3.75 mm, and 11.52+/-4.33 mm, respectively. Prediction of couch adjustment in LAT, SI, and AP coordinates from CBCT tracking agrees with the actual clinical couch correction within 0.92+/-0.74 mm, 1.37+/-1.26 mm, and 0.68+/-0.56 mm for pancreas cases and within 1.12+/-0.96 mm, 1.15+/-0.92 mm and 0.90+/-0.86 mm for liver cases, respectively. Conclusion: Tracking pre-treatment CBCT projections using template matching and sequential stereo triangulation is suitable for assessing fiducial motion and adjusting the patient setup for abdominal SBRT. CBCT can be used for motion modeling, potentially eliminating the need for additional fluoroscopic pair acquisition and thus reducing the imaging dose to the patient and the total treatment time.

physics.med-ph↗

arXiv2021

Deep Diffusion Processes for Active Learning of Hyperspectral Images

A method for active learning of hyperspectral images (HSI) is proposed, which combines deep learning with diffusion processes on graphs. A deep variational autoencoder extracts smoothed, denoised features from a high-dimensional HSI, which are then used to make labeling queries based on graph diffusion processes. The proposed method combines the robust representations of deep learning with the mathematical tractability of diffusion geometry, and leads to strong performance on real HSI.

cs.CV↗

arXiv2020

Balancing Geometry and Density: Path Distances on High-Dimensional Data

New geometric and computational analyses of power-weighted shortest-path distances (PWSPDs) are presented. By illuminating the way these metrics balance density and geometry in the underlying data, we clarify their key parameters and discuss how they may be chosen in practice. Comparisons are made with related data-driven metrics, which illustrate the broader role of density in kernel-based unsupervised and semi-supervised machine learning. Computationally, we relate PWSPDs on complete weighted graphs to their analogues on weighted nearest neighbor graphs, providing high probability guarantees on their equivalence that are near-optimal. Connections with percolation theory are developed to establish estimates on the bias and variance of PWSPDs in the finite sample setting. The theoretical results are bolstered by illustrative experiments, demonstrating the versatility of PWSPDs for a wide range of data settings. Throughout the paper, our results require only that the underlying data is sampled from a low-dimensional manifold, and depend crucially on the intrinsic dimension of this manifold, rather than its ambient dimension.

stat.ML↗

arXiv2018

QUBIC: Exploring the primordial Universe with the Q\&U Bolometric Interferometer

In this paper we describe QUBIC, an experiment that will observe the polarized microwave sky with a novel approach, which combines the sensitivity of state-of-the art bolometric detectors with the systematic effects control typical of interferometers. QUBIC unique features are the so-called "self-calibration", a technique that allows us to clean the measured data from instrumental effects, and its spectral imaging power, i.e. the ability to separate the signal in various sub-bands within each frequency band. QUBIC will observe the sky in two main frequency bands: 150 GHz and 220 GHz. A technological demonstrator is currently under testing and will be deployed in Argentina during 2019, while the final instrument is expected to be installed during 2020.

astro-ph.IM↗

arXiv2018

Map matching when the map is wrong: Efficient vehicle tracking on- and off-road for map learning

Given a sequence of possibly sparse and noisy GPS traces and a map of the road network, map matching algorithms can infer the most accurate trajectory on the road network. However, if the road network is wrong (for example due to missing or incorrectly mapped roads, missing parking lots, misdirected turn restrictions or misdirected one-way streets) standard map matching algorithms fail to reconstruct the correct trajectory. In this paper, an algorithm to tracking vehicles able to move both on and off the known road network is formulated. It efficiently unifies existing hidden Markov model (HMM) approaches for map matching and standard free-space tracking methods (e.g. Kalman smoothing) in a principled way. The algorithm is a form of interacting multiple model (IMM) filter subject to an additional assumption on the type of model interaction permitted, termed here as semi-interacting multiple model (sIMM) filter. A forward filter (suitable for real-time tracking) and backward MAP sampling step (suitable for MAP trajectory inference and map matching) are described. The framework set out here is agnostic to the specific tracking models used, and makes clear how to replace these components with others of a similar type. In addition to avoiding generating misleading map matching trajectories, this algorithm can be applied to learn map features by detecting unmapped or incorrectly mapped roads and parking lots, incorrectly mapped turn restrictions and road directions.

math.OC↗

arXiv2018

Two-Stage Residual Inclusion under the Additive Hazards Model - An Instrumental Variable Approach with Application to SEER-Medicare Linked Data

Instrumental variable is an essential tool for addressing unmeasured confounding in observational studies. Two stage predictor substitution (2SPS) estimator and two stage residual inclusion(2SRI) are two commonly used approaches in applying instrumental variables. Recently 2SPS was studied under the additive hazards model in the presence of competing risks of time-to-events data, where linearity was assumed for the relationship between the treatment and the instrument variable. This assumption may not be the most appropriate when we have binary treatments. In this paper, we consider the 2SRI estimator under the additive hazards model for general survival data and in the presence of competing risks, which allows generalized linear models for the relation between the treatment and the instrumental variable. We derive the asymptotic properties including a closed-form asymptotic variance estimate for the 2SRI estimator. We carry out numerical studies in finite samples, and apply our methodology to the linked Surveillance, Epidemiology and End Results (SEER) - Medicare database comparing radical prostatectomy versus conservative treatment in early-stage prostate cancer patients.

stat.AP↗

arXiv2017

High-Dimensional Variable Selection and Prediction under Competing Risks with Application to SEER-Medicare Linked Data

Competing risk analysis considers event times due to multiple causes, or of more than one event types. Commonly used regression models for such data include 1) cause-specific hazards model, which focuses on modeling one type of event while acknowledging other event types simultaneously; and 2) subdistribution hazards model, which links the covariate effects directly to the cumulative incidence function. Their use and in particular statistical properties in the presence of high-dimensional predictors are largely unexplored. Motivated by an analysis using the linked SEER-Medicare database for the purposes of predicting cancer versus non-cancer mortality for patients with prostate cancer, we study the accuracy of prediction and variable selection of existing statistical learning methods under both models using extensive simulation experiments, including different approaches to choosing penalty parameters in each method. We then apply the optimal approaches to the analysis of the SEER-Medicare data.

stat.AP↗

arXiv2013

Benders, Nested Benders and Stochastic Programming: An Intuitive Introduction

This article aims to explain the Nested Benders algorithm for the solution of large-scale stochastic programming problems in a way that is intelligible to someone coming to it for the first time. In doing so it gives an explanation of Benders decomposition and of its application to two-stage stochastic programming problems (also known in this context as the L-shaped method), then extends this to multi-stage problems as the Nested Benders algorithm. The article is aimed at readers with some knowledge of linear and possibly stochastic programming but aims to develop most concepts from simple principles in an understandable way. The focus is on intuitive understanding rather than rigorous proofs.

math.OC↗