Teaghan O'Briain

Teaghan O'Briain, Carlos Uribe, Kwang Moo Yi et al.

To correct for respiratory motion in PET imaging, an interpretable and unsupervised deep learning technique, FlowNet-PET, was constructed. The network was trained to predict the optical flow between two PET frames from different breathing amplitude ranges. The trained model aligns different retrospectively-gated PET images, providing a final image with similar counting statistics as a non-gated image, but without the blurring effects. FlowNet-PET was applied to anthropomorphic digital phantom data, which provided the possibility to design robust metrics to quantify the corrections. When comparing the predicted optical flows to the ground truths, the median absolute error was found to be smaller than the pixel and slice widths. The improvements were illustrated by comparing against images without motion and computing the intersection over union (IoU) of the tumors as well as the enclosed activity and coefficient of variation (CoV) within the no-motion tumor volume before and after the corrections were applied. The average relative improvements provided by the network were 64%, 89%, and 75% for the IoU, total activity, and CoV, respectively. FlowNet-PET achieved similar results as the conventional retrospective phase binning approach, but only required one sixth of the scan duration. The code and data have been made publicly available (https://github.com/teaghan/FlowNet_PET).

Teaghan O'Briain, Yuan-Sen Ting, Sébastien Fabbro et al.

We discuss how to achieve mapping from large sets of imperfect simulations and observational data with unsupervised domain adaptation. Under the hypothesis that simulated and observed data distributions share a common underlying representation, we show how it is possible to transfer between simulated and observed domains. Driven by an application to interpret stellar spectroscopic sky surveys, we construct the domain transfer pipeline from two adversarial autoencoders on each domains with a disentangling latent space, and a cycle-consistency constraint. We then construct a differentiable pipeline from physical stellar parameters to realistic observed spectra, aided by a supplementary generative surrogate physics emulator network. We further exemplify the potential of the method on the reconstructed spectra quality and to discover new spectral features associated to elemental abundances.

Teaghan O'Briain, Yuan-Sen Ting, Sébastien Fabbro et al.

The advancements in stellar spectroscopy data acquisition have made it necessary to accomplish similar improvements in efficient data analysis techniques. Current automated methods for analyzing spectra are either (a) data-driven, which requires prior knowledge of stellar parameters and elemental abundances, or (b) based on theoretical synthetic models that are susceptible to the gap between theory and practice. In this study, we present a hybrid generative domain adaptation method that turns simulated stellar spectra into realistic spectra by applying unsupervised learning to large spectroscopic surveys. We apply our technique to the APOGEE H-band spectra at R=22,500 and the Kurucz synthetic models. As a proof of concept, two case studies are presented. The first of which is the calibration of synthetic data to become consistent with observations. To accomplish this, synthetic models are morphed into spectra that resemble observations, thereby reducing the gap between theory and observations. Fitting the observed spectra shows an improved average reduced $χ_R^2$ from 1.97 to 1.22, along with a reduced mean residual from 0.16 to -0.01 in normalized flux. The second case study is the identification of the elemental source of missing spectral lines in the synthetic modelling. A mock dataset is used to show that absorption lines can be recovered when they are absent in one of the domains. This method can be applied to other fields, which use large data sets and are currently limited by modelling accuracy. The code used in this study is made publicly available on github.

Teaghan O'Briain, Kyong Hwan Jin, Hongyoon Choi et al.

We aim to reduce the tedious nature of developing and evaluating methods for aligning PET-CT scans from multiple patient visits. Current methods for registration rely on correspondences that are created manually by medical experts with 3D manipulation, or assisted alignments done by utilizing mutual information across CT scans that may not be consistent when transferred to the PET images. Instead, we propose to label multiple key points across several 2D slices, which we then fit a key curve to. This removes the need for creating manual alignments in 3D and makes the labelling process easier. We use these key curves to define an error metric for the alignments that can be computed efficiently. While our metric is non-differentiable, we further show that we can utilize it during the training of our deep model via a novel method. Specifically, instead of relying on detailed geometric labels -- e.g., manual 3D alignments -- we use synthetically generated deformations of real data. To incorporate robustness to changes that occur between visits other than geometric changes, we enforce consistency across visits in the deep network's internal representations. We demonstrate the potential of our method via qualitative and quantitative experiments.