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Daniel O'Connor

Publications and source records attributed to Daniel O'Connor.

17 recordsLinked to original sources

Sequential Reservoir Computing for Efficient High-Dimensional Spatiotemporal Forecasting

Forecasting high-dimensional spatiotemporal systems remains computationally challenging for recurrent neural networks (RNNs) and long short-term memory (LSTM) models due to gradient-based training and memory bottlenecks. Reservoir Computing (RC) mitigates these challenges by replacing backpropagation with fixed recurrent layers and a convex readout optimization, yet conventional RC architectures still scale poorly with input dimensionality. We introduce a Sequential Reservoir Computing (Sequential RC) architecture that decomposes a large reservoir into a series of smaller, interconnected reservoirs. This design reduces memory and computational costs while preserving long-term temporal dependencies. Using both low-dimensional chaotic systems (Lorenz63) and high-dimensional physical simulations (2D vorticity and shallow-water equations), Sequential RC achieves 15-25% longer valid forecast horizons, 20-30% lower error metrics (SSIM, RMSE), and up to three orders of magnitude lower training cost compared to LSTM and standard RNN baselines. The results demonstrate that Sequential RC maintains the simplicity and efficiency of conventional RC while achieving superior scalability for high-dimensional dynamical systems. This approach provides a practical path toward real-time, energy-efficient forecasting in scientific and engineering applications.

cs.LG

Accelerated Patient-specific Non-Cartesian MRI Reconstruction using Implicit Neural Representations

The scanning time for a fully sampled MRI can be undesirably lengthy. Compressed sensing has been developed to minimize image artifacts in accelerated scans, but the required iterative reconstruction is computationally complex and difficult to generalize on new cases. Image-domain-based deep learning methods (e.g., convolutional neural networks) emerged as a faster alternative but face challenges in modeling continuous k-space, a problem amplified with non-Cartesian sampling commonly used in accelerated acquisition. In comparison, implicit neural representations can model continuous signals in the frequency domain and thus are compatible with arbitrary k-space sampling patterns. The current study develops a novel generative-adversarially trained implicit neural representations (k-GINR) for de novo undersampled non-Cartesian k-space reconstruction. k-GINR consists of two stages: 1) supervised training on an existing patient cohort; 2) self-supervised patient-specific optimization. In stage 1, the network is trained with the generative-adversarial network on diverse patients of the same anatomical region supervised by fully sampled acquisition. In stage 2, undersampled k-space data of individual patients is used to tailor the prior-embedded network for patient-specific optimization. The UCSF StarVIBE T1-weighted liver dataset was evaluated on the proposed framework. k-GINR is compared with an image-domain deep learning method, Deep Cascade CNN, and a compressed sensing method. k-GINR consistently outperformed the baselines with a larger performance advantage observed at very high accelerations (e.g., 20 times). k-GINR offers great value for direct non-Cartesian k-space reconstruction for new incoming patients across a wide range of accelerations liver anatomy.

eess.IV

Multi-coil Magnetic Resonance Imaging with Compressed Sensing Using Physically Motivated Regularization

With the advent of multi-coil imaging and compressed sensing, a number of model based reconstruction algorithms have been created. They incorporate a multitude of different regularization functions based on physics, observed phenomenology, and heuristics. Moreover, several iterative methods exist that attempt to simultaneously estimate the sensitivity maps and the image. In this manuscript, we present a generalization of several existing iterative model based algorithms. We devise a calibrationless instance of this generalization that only incorporates regularization terms based on physics and the accepted compressed sensing phenomenology of sparsity in the wavelet domain. We compare the results of the new amalgamated optimization problem with existing methods on both simulated and real datasets. We show that the images reconstructed using the new method, entitled Multi-coil Compressed Sensing (MCCS), are of higher quality than existing methods in all cases studied.

eess.IV

Thermal and dimensional evaluation of a test plate for assessing the measurement capability of a thermal imager within nuclear decommissioning storage

In this laboratory-based study, a plate was designed, manufactured and then characterised thermally and dimensionally using a thermal imager. This plate comprised a range of known scratch, dent, thinning and pitting artefacts as mimics of possible surface anomalies, as well as an arrangement of higher emissivity targets. The thermal and dimensional characterisation of this plate facilitated surface temperature determination. This was verified through thermal models and successful defect identification of the scratch and pitting artefacts at temperatures from \SIrange{30}{170}{\celsius}. These laboratory measurements demonstrated the feasibility of deploying in-situ thermal imaging to the thermal and dimensional characterisation of special nuclear material containers. Surface temperature determination demonstrated uncertainties from \SIrange{1.0}{6.8}{\celsius} (\(k = 2\)). The principle challenges inhibiting successful deployment are a lack of suitable emissivity data and a robust defect identification algorithm suited to both static and transient datasets.

physics.ins-det

The Perturbed Ferromagnetic Chain: A Tuneable Test of Quantum Hardness in the Transverse-Field Ising Model

Quantum annealing in the transverse-field Ising model (TFIM) with open-system dynamics is known to use thermally-assisted tunneling to drive computation. However, it is still subject to debate whether quantum systems in the presence of decoherence are more useful than those using classical dynamics to drive computation. We contribute to this debate by introducing the perturbed ferromagnetic chain (PFC), a chain of frustrated sub-systems where the degree of frustration scales inversely with the perturbation introduced by a tunable parameter. This gives us an easily embeddable gadget whereby problem hardness can be tuned for systems of constant size. We outline the properties of the PFC and compare classical spin-vector Monte Carlo (SVMC) variants with the adiabatic quantum master equation. We demonstrate that SVMC methods get trapped in the exponentially large first-excited-state manifold when solving this frustrated problem, whereas evolution using quantum dynamics remains in the lowest energy eigenstates. This results in significant differences in ground state probability when using either classical or quantum annealing dynamics in the TFIM.

quant-ph

Locally Suppressed Transverse-Field Protocol for Diabatic Quantum Annealing

Diabatic quantum annealing (DQA) is an alternative algorithm to adiabatic quantum annealing (AQA) that can be used to circumvent the exponential slowdown caused by small minima in the annealing energy spectrum. We present the locally suppressed transverse-field (LSTF) protocol, a heuristic method for making stoquastic optimization problems compatible with DQA. We show that, provided an optimization problem intrinsically has magnetic frustration due to inhomogeneous local fields, a target qubit in the problem can always be manipulated to create a double minimum in the energy gap between the ground and first excited states during the evolution of the algorithm. Such a double energy minimum can be exploited to induce diabatic transitions to the first excited state and back to the ground state. In addition to its relevance to classical and quantum algorithmic speed-ups, the LSTF protocol enables DQA proof-of-principle and physics experiments to be performed on existing hardware, provided independent controls exist for the transverse qubit magnetization fields. We discuss the implications on the coherence requirements of the quantum annealing hardware when using the LSTF protocol, considering specifically the cases of relaxation and dephasing. We show that the relaxation rate of a large system can be made to depend only on the target qubit presenting new opportunities for the characterization of the decohering environment in a quantum annealing processor.

quant-ph

RBM-Flow and D-Flow: Invertible Flows with Discrete Energy Base Spaces

Efficient sampling of complex data distributions can be achieved using trained invertible flows (IF), where the model distribution is generated by pushing a simple base distribution through multiple non-linear bijective transformations. However, the iterative nature of the transformations in IFs can limit the approximation to the target distribution. In this paper we seek to mitigate this by implementing RBM-Flow, an IF model whose base distribution is a Restricted Boltzmann Machine (RBM) with a continuous smoothing applied. We show that by using RBM-Flow we are able to improve the quality of samples generated, quantified by the Inception Scores (IS) and Frechet Inception Distance (FID), over baseline models with the same IF transformations, but with less expressive base distributions. Furthermore, we also obtain D-Flow, an IF model with uncorrelated discrete latent variables. We show that D-Flow achieves similar likelihoods and FID/IS scores to those of a typical IF with Gaussian base variables, but with the additional benefit that global features are meaningfully encoded as discrete labels in the latent space.

cs.LG

Least Squares Optimal Density Compensation for the Gridding Non-uniform Discrete Fourier Transform

The Gridding algorithm has shown great utility for reconstructing images from non-uniformly spaced samples in the Fourier domain in several imaging modalities. Due to the non-uniform spacing, some correction for the variable density of the samples must be made. Existing methods for generating density compensation values are either sub-optimal or only consider a finite set of points (a set of measure 0) in the optimization. This manuscript presents the first density compensation algorithm for a general trajectory that takes into account the point spread function over a set of non-zero measure. We show that the images reconstructed with Gridding using the density compensation values of this method are of superior quality when compared to density compensation weights determined in other ways. Results are shown with a numerical phantom and with magnetic resonance images of the abdomen and the knee.

eess.IV

Utilizing the Wavelet Transform's Structure in Compressed Sensing

Compressed sensing has empowered quality image reconstruction with fewer data samples than previously though possible. These techniques rely on a sparsifying linear transformation. The Daubechies wavelet transform is a common sparsifying transformation used for this purpose. In this work, we take advantage of the structure of this wavelet transform and identify an affine transformation that increases the sparsity of the result. After inclusion of this affine transformation, we modify the resulting optimization problem to comply with the form of the Basis Pursuit Denoising problem. Finally, we show theoretically that this yields a lower bound on the error of the reconstruction and present results where solving this modified problem yields images of higher quality for the same sampling patterns.

eess.IV

Fast Variable Density Poisson-Disc Sample Generation with Directional Variation

We present a fast method for generating random samples according to a variable density Poisson-disc distribution. A minimum threshold distance is used to create a background grid array for keeping track of those points that might affect any new candidate point; this reduces the number of conflicts that must be checked before acceptance of a new point, thus reducing the number of computations required. We demonstrate the algorithm's ability to generate variable density Poisson-disc sampling patterns according to a parameterized function, including patterns where the variations in density are a function of direction. We further show that these sampling patterns are appropriate for compressed sensing applications. Finally, we present a method to generate patterns with a specific acceleration rate.

eess.IV

Di-chromatic Interpolation of Magnetic Resonance Metabolic Imagery

Magnetic resonance imaging with hyperpolarized contrast agents can provide unprecedented \textit{in-vivo} measurements of metabolism, but yields images that are lower resolution than that achieved with proton anatomical imaging. In order to spatially localize the metabolic activity, the metabolic image must be interpolated to the size of the proton image. The most common methods for choosing the unknown values rely exclusively on values of the original un-interpolated image. In this work, we present an alternative method that uses the higher-resolution proton image to provide additional spatial structure. The interpolated image is the result of a convex optimization algorithm which is solved with the Fast Iterative Shrinkage Threshold Algorithm (FISTA). Results are shown with images of hyperpolarized pyruvate, lactate, and bicarbonate using data of the heart and brain from healthy human volunteers, a healthy porcine heart, and a human with prostate cancer.

eess.IV

Slide-free MUSE Microscopy to H&E Histology Modality Conversion via Unpaired Image-to-Image Translation GAN Models

MUSE is a novel slide-free imaging technique for histological examination of tissues that can serve as an alternative to traditional histology. In order to bridge the gap between MUSE and traditional histology, we aim to convert MUSE images to resemble authentic hematoxylin- and eosin-stained (H&E) images. We evaluated four models: a non-machine-learning-based color-mapping unmixing-based tool, CycleGAN, DualGAN, and GANILLA. CycleGAN and GANILLA provided visually compelling results that appropriately transferred H&E style and preserved MUSE content. Based on training an automated critic on real and generated H&E images, we determined that CycleGAN demonstrated the best performance. We have also found that MUSE color inversion may be a necessary step for accurate modality conversion to H&E. We believe that our MUSE-to-H&E model can help improve adoption of novel slide-free methods by bridging a perceptual gap between MUSE imaging and traditional histology.

eess.IV

Motion Compensated Dynamic MRI Reconstruction with Local Affine Optical Flow Estimation

This paper proposes a novel framework to reconstruct the dynamic magnetic resonance images (DMRI) with motion compensation (MC). Due to the inherent motion effects during DMRI acquisition, reconstruction of DMRI using motion estimation/compensation (ME/MC) has been studied under a compressed sensing (CS) scheme. In this paper, by embedding the intensity-based optical flow (OF) constraint into the traditional CS scheme, we are able to couple the DMRI reconstruction with motion field estimation. The formulated optimization problem is solved by a primal-dual algorithm with linesearch due to its efficiency when dealing with non-differentiable problems. With the estimated motion field, the DMRI reconstruction is refined through MC. By employing the multi-scale coarse-to-fine strategy, we are able to update the variables(temporal image sequences and motion vectors) and to refine the image reconstruction alternately. Moreover, the proposed framework is capable of handling a wide class of prior information (regularizations) for DMRI reconstruction, such as sparsity, low rank and total variation. Experiments on various DMRI data, ranging from in vivo lung to cardiac dataset, validate the reconstruction quality improvement using the proposed scheme in comparison to several state-of-the-art algorithms.

cs.CV

Breaking the Span Assumption Yields Fast Finite-Sum Minimization

In this paper, we show that SVRG and SARAH can be modified to be fundamentally faster than all of the other standard algorithms that minimize the sum of $n$ smooth functions, such as SAGA, SAG, SDCA, and SDCA without duality. Most finite sum algorithms follow what we call the "span assumption": Their updates are in the span of a sequence of component gradients chosen in a random IID fashion. In the big data regime, where the condition number $κ=\mathcal{O}(n)$, the span assumption prevents algorithms from converging to an approximate solution of accuracy $ε$ in less than $n\ln(1/ε)$ iterations. SVRG and SARAH do not follow the span assumption since they are updated with a hybrid of full-gradient and component-gradient information. We show that because of this, they can be up to $Ω(1+(\ln(n/κ))_+)$ times faster. In particular, to obtain an accuracy $ε= 1/n^α$ for $κ=n^β$ and $α,β\in(0,1)$, modified SVRG requires $\mathcal{O}(n)$ iterations, whereas algorithms that follow the span assumption require $\mathcal{O}(n\ln(n))$ iterations. Moreover, we present lower bound results that show this speedup is optimal, and provide analysis to help explain why this speedup exists. With the understanding that the span assumption is a point of weakness of finite sum algorithms, future work may purposefully exploit this to yield even faster algorithms in the big data regime.

math.OC

Fraction-variant beam orientation optimization for non-coplanar IMRT

Conventional beam orientation optimization (BOO) algorithms for IMRT assume that the same set of beam angles is used for all treatment fractions. In this paper we present a BOO formulation based on group sparsity that simultaneously optimizes non-coplanar beam angles for all fractions, yielding a fraction-variant (FV) treatment plan. Beam angles are selected by solving a multi-fraction FMO problem involving 500-700 candidate beams per fraction, with an additional group sparsity term that encourages most candidate beams to be inactive. The optimization problem is solved using the Fast Iterative Shrinkage-Thresholding Algorithm. Our FV BOO algorithm is used to create non-coplanar, five-fraction treatment plans for prostate and lung cases, as well as a non-coplanar 30-fraction plan for a head and neck case. A homogeneous PTV dose coverage is maintained in all fractions. The treatment plans are compared with fraction-invariant plans that use a fixed set of beam angles for all fractions. The FV plans reduced mean and max OAR dose on average by 3.3% and 3.7% of the prescription dose, respectively. Notably, mean OAR dose was reduced by 14.3% of prescription dose (rectum), 11.6% (penile bulb), 10.7% (seminal vesicle), 5.5% (right femur), 3.5% (bladder), 4.0% (normal left lung), 15.5% (cochleas), and 5.2% (chiasm). Max OAR dose was reduced by 14.9% of prescription dose (right femur), 8.2% (penile bulb), 12.7% (prox. bronchus), 4.1% (normal left lung), 15.2% (cochleas), 10.1% (orbits), 9.1% (chiasm), 8.7% (brainstem), and 7.1% (parotids). Meanwhile, PTV homogeneity defined as D95/D5 improved from .95 to .98 (prostate case) and from .94 to .97 (lung case), and remained constant for the head and neck case. Moreover, the FV plans are dosimetrically similar to conventional plans that use twice as many beams per fraction. Thus, FV BOO offers the potential to reduce delivery time for non-coplanar IMRT.

physics.med-ph

Fast non-coplanar beam orientation optimization based on group sparsity

The selection of beam orientations, which is a key step in radiation treatment planning, is particularly challenging for non-coplanar radiotherapy systems due to the large number of candidate beams. In this paper, we report progress on the group sparsity approach to beam orientation optimization, wherein beam angles are selected by solving a large scale fluence map optimization problem with an additional group sparsity penalty term that encourages most candidate beams to be inactive. The optimization problem is solved using an accelerated proximal gradient method, the Fast Iterative Shrinkage-Thresholding Algorithm (FISTA). We derive a closed-form expression for a relevant proximal operator which enables the application of FISTA. The proposed algorithm is used to create non-coplanar treatment plans for four cases (including head and neck, lung, and prostate cases), and the resulting plans are compared with clinical plans. The dosimetric quality of the group sparsity treatment plans is superior to that of the clinical plans. Moreover, the runtime for the group sparsity approach is typically about 5 minutes. Problems of this size could not be handled using the previous group sparsity method for beam orientation optimization, which was slow to solve much smaller coplanar cases. This work demonstrates for the first time that the group sparsity approach, when combined with an accelerated proximal gradient method such as FISTA, works effectively for non-coplanar cases with 500-800 candidate beams.

physics.med-ph

Regarding the "Comments on 'Near-field interference for the unidirectional excitation of electromagnetic guided modes' " by Lee et al

We would like to clarify the misunderstanding caused by comment [arXiv:1306.5068 (2013)] on our article [Science 340, 328 (2013)]. The vectorial near-field interference effect described in our article is a fundamental physical process valid for all kinds of waves, both photonic and plasmonic, and the discovery of this effect is the main topic of the paper. The experiment using a slit in a metal film was one possible practical realization, but the effect has recently been experimentally validated in several other structures, as described in this reply.

physics.optics