arXiv subjects

Jonathan Miller

Publications and source records attributed to Jonathan Miller.

12 recordsLinked to original sources

arXiv2024

On-Chip Verified Quantum Computation with an Ion-Trap Quantum Processing Unit

We present and experimentally demonstrate a novel approach to verification and benchmarking of quantum computing, implementing it on an ion-trap quantum computer. Unlike previous information-theoretically secure verification protocols, which typically require quantum communication between client and server, our approach is implemented entirely on-chip. This eliminates the need for a quantum client and significantly enhances practicality. We perform tomography to justify the additionally required assumption that the noise is independent of the secret used to prepare the Server's single-qubit states. We quantify the soundness error which may be caused by residual secret dependencies. We demonstrate our protocol on the 20-qubit Quantinuum H1-1 ion-trap quantum processing unit, using qubit measurements and resets to construct measurement patterns with up to 52 vertices. To our knowledge, these are the largest verified measurement-based quantum computations performed to date. Our results pave the way for more accessible and efficient verification and benchmarking strategies in near-term quantum devices, enabling robust performance assessment without the added cost of external quantum infrastructure.

quant-ph↗

arXiv2020

Inferring Convolutional Neural Networks' accuracies from their architectural characterizations

Convolutional Neural Networks (CNNs) have shown strong promise for analyzing scientific data from many domains including particle imaging detectors. However, the challenge of choosing the appropriate network architecture (depth, kernel shapes, activation functions, etc.) for specific applications and different data sets is still poorly understood. In this paper, we study the relationships between a CNN's architecture and its performance by proposing a systematic language that is useful for comparison between different CNN's architectures before training time. We characterize CNN's architecture by different attributes, and demonstrate that the attributes can be predictive of the networks' performance in two specific computer vision-based physics problems -- event vertex finding and hadron multiplicity classification in the MINERvA experiment at Fermi National Accelerator Laboratory. In doing so, we extract several architectural attributes from optimized networks' architecture for the physics problems, which are outputs of a model selection algorithm called Multi-node Evolutionary Neural Networks for Deep Learning (MENNDL). We use machine learning models to predict whether a network can perform better than a certain threshold accuracy before training. The models perform 16-20% better than random guessing. Additionally, we found an coefficient of determination of 0.966 for an Ordinary Least Squares model in a regression on accuracy over a large population of networks.

cs.CV↗

arXiv2017

Exotic Trajectories Effects on Neutrino Oscillations

Recently, for the first time, exotic loop trajectories were observed in a photon triple slit experiment. We discuss possible origins and potential impacts of analogical exotic trajectories in neutrino production, propagation and detection onto the neutrino oscillation observables.

hep-ph↗

arXiv2015

Orthologs from maxmer sequence context

Context-dependent identification of orthologs customarily relies on conserved gene order or whole-genome sequence alignment. It is shown here that short-range context--as short as single maximal matches--also provides an effective means to identify orthologs within whole genomes. On pristine (un-repeatmasked) mammalian whole-genome assemblies we perform a genome "intersection" that in general consumes less than one thirtieth of the computation time required by commonly used methods for whole-genome alignment, and we extract "non-embedded maximal matches," maximal matches that are not embedded into other maximal matches, as potential orthologs. An ortholog identified via non-embedded maximal matches is analogous to a "positional ortholog" or a "primary ortholog" as defined in previous literature; such orthologs constitute homologs derived from the same direct ancestor whose ancestral positions in the genome are conserved. At the nucleotide level, non-embedded maximal matches recapitulate most exact matches identified by a Lastz net alignment. At the gene level, reciprocal best hits of genes containing non-embedded maximal matches recover one-to-one orthologs annotated by Ensembl Compara with high selectivity and high sensitivity; these reciprocal best hits additionally include putatively novel orthologs not found in Ensembl (e.g. over two thousand for human/chimpanzee). The method is especially suitable for genome-wide identification of orthologs.

q-bio.QM↗

arXiv2014

Human-chimpanzee alignment: Ortholog Exponentials and Paralog Power Laws

Genomic subsequences conserved between closely related species such as human and chimpanzee exhibit an exponential length distribution, in contrast to the algebraic length distribution observed for sequences shared between distantly related genomes. We find that the former exponential can be further decomposed into an exponential component primarily composed of orthologous sequences, and a truncated algebraic component primarily composed of paralogous sequences.

q-bio.GN↗

arXiv2013

Quasi-classical Gravity effect on neutrino oscillations in a gravitational field of an heavy astrophysical object

In the framework of quantum field theory, a graviton interacts locally with a quantum state having definite mass, i.e. the gravitational mass eigenstate, while a weak boson interacts with a state having definite flavor, i.e. the flavor eigenstate. An interaction of a neutrino with an energetic graviton may trigger the collapse of the neutrino to a definite mass eigenstate with probability expressed in terms of PMNS mixing matrix elements. Thus, gravitons would induce quantum decoherence of a coherent neutrino flavor state similarly to how weak bosons induce quantum decoherence of a neutrino in a definite mass state. We demonstrate that such an essentially quantum gravity effect may have strong consequences for neutrino oscillation phenomena in astrophysics due to relatively large scattering cross sections of relativistic neutrinos undergoing large-angle radiation of energetic gravitons in gravitational field of a classical massive source (i.e. the quasi-classical case of gravitational Bethe-Heitler scattering). This graviton-induced {\it decoherence} is compared to {\it decoherence} due to propagation in the presence of the Earth matter effect. Based on this study, we propose a new technique for the indirect detection of energetic gravitons by measuring the flavor composition of astrophysical neutrinos.

hep-ph↗

arXiv2011

An Algorithm for Detecting Intrinsically Knotted Graphs

We describe an algorithm that recognizes some (perhaps all) intrinsically knotted (IK) graphs, and can help find knotless embeddings for graphs that are not IK. The algorithm, implemented as a Mathematica program, has already been used by Goldberg, Mattman, and Naimi [6] to greatly expand the list of known minor minimal IK graphs, and to find knotless embeddings for some graphs that had previously resisted attempts to classify them as IK or non-IK.

math.GT↗

arXiv2001

Identifying Proteins of High Designability via Surface-Exposure Patterns

Using an off-lattice model, we fully enumerate folded conformations of polypeptide chains of up to N = 19 monomers. Structures are found to differ markedly in designability, defined as the number of sequences with that structure as a unique lowest-energy conformation. We find that designability is closely correlated with the pattern of surface exposure of the folded structure. For longer chains, complete enumeration of structures is impractical. Instead, structures can be randomly sampled, and relative designability estimated either from designability within the random sample, or directly from surface-exposure pattern. We compare the surface-exposure patterns of those structures identified as highly designable to the patterns of naturally occurring proteins.

cond-mat.soft↗

arXiv2000

Symmetry and designability for lattice protein models

Native protein folds often have a high degree of symmetry. We study the relationship between the symmetries of native proteins, and their designabilities -- how many different sequences encode a given native structure. Using a two-dimensional lattice protein model based on hydrophobicity, we find that those native structures that are encoded by the largest number of different sequences have high symmetry. However only certain symmetries are enhanced, e.g. x/y-mirror symmetry and $180^o$ rotation, while others are suppressed. If it takes a large number of mutations to destabilize the native state of a protein, then, by definition, the state is highly designable. Hence, our findings imply that insensitivity to mutation implies high symmetry. It appears that the relationship between designability and symmetry results because protein substructures are also designable. Native protein folds may therefore be symmetric because they are composed of repeated designable substructures.

cond-mat.stat-mech↗

arXiv1999

Non-fermi liquid as passive scalar fluid

I suggest that electron localization by random flux and passive transport in quenched velocity fields in two dimensions be studied as perturbations of the simple operator ${\cal K}={\bf A} \cdot \nabla$, with incompressible velocity field/vector potential ${\bf A}=\nabla \times ϕ=(-\partial_y,\partial_x)ϕ$. This operator has an infinitely degenerate subspace of zero energy eigenstates, arising from incompressibility, that are {\it extended} for generic $ϕ({\bf x})$ and are expected to remain so under perturbation. I propose that an anomaly accounts qualitatively for properties of the spectrum and eigenstates of ${\cal K}$ and its perturbations.

cond-mat.mes-hall↗

arXiv1995

Tunneling edges at strong disorder

Scattering between edge states that bound one-dimensional domains of opposite potential or flux is studied, in the presence of strong potential or flux disorder. A mobility edge is found as a function of disorder and energy, and we have characterized the extended phase. "paper_FINAL.tex" 439 lines, 20366 characters In the presence of flux and/or potential disorder, the localization length scales exponentially with the width of the barrier. We discuss implications for the random-flux problem.

cond-mat↗

arXiv1995

Passive scalars, random flux, and chiral phase fluids

We study the two-dimensional localization problem for (i) a classical diffusing particle advected by a quenched random mean-zero vorticity field, and (ii) a quantum particle in a quenched random mean-zero magnetic field. Through a combination of numerical and analytic techniques we argue that both systems have extended eigenstates at a special point in the spectrum, $E_c$, where a sublattice decomposition obtains. In a neighborhood of this point, the Lyapunov exponents of the transfer-matrices acquire ratios characteristic of conformal invariance allowing an indirect determination of $1/r$ for the typical spatial decay of eigenstates.

cond-mat↗