Fast Fourier Optimization: Sparsity Matters

Many interesting and fundamentally practical optimization problems, ranging from optics, to signal processing, to radar and acoustics, involve constraints on the Fourier transform of a function. It is well-known that the {\em fast Fourier transform} (fft) is a recursive algorithm that can dramatically improve the efficiency for computing the discrete Fourier transform. However, because it is recursive, it is difficult to embed into a linear optimization problem. In this paper, we explain the main idea behind the fast Fourier transform and show how to adapt it in such a manner as to make it encodable as constraints in an optimization problem. We demonstrate a real-world problem from the field of high-contrast imaging. On this problem, dramatic improvements are translated to an ability to solve problems with a much finer grid of discretized points. As we shall show, in general, the "fast Fourier" version of the optimization constraints produces a larger but sparser constraint matrix and therefore one can think of the fast Fourier transform as a method of sparsifying the constraints in an optimization problem, which is usually a good thing.Comment: 16 pages, 8 figure

Torpor in marsupials: Recent advances

We report new findings about torpor in marsupials with regard to three energy demanding processes: (i) development and growth, (ii) reproduction, and (iii) rewarming. Young marsupials use torpor extensively after they develop endothermy, and torpor is generally deeper and longer than in the same individuals when they reach adult size. Adult marsupials also employ torpor during pregnancy and/or lactation to reduce energy expenditure and perhaps to store fat for later use. Moreover, to enhance the energy-conserving potential of torpor, desert marsupials bask during arousal to minimize energy costs of rewarming. We show that the functions of torpor extend beyond merely reducing energy expenditure during food shortages and that torpor can save substantial amounts of energy even during the rewarming process

Accurate and efficient method for the treatment of exchange in a plane-wave basis.

Published versio

Hierarchical search strategy for the detection of gravitational waves from coalescing binaries: Extension to post-Newtonian wave forms

The detection of gravitational waves from coalescing compact binaries would be a computationally intensive process if a single bank of template wave forms (i.e., a one step search) is used. In an earlier paper we had presented a detection strategy, called a two step search}, that utilizes a hierarchy of template banks. It was shown that in the simple case of a family of Newtonian signals, an on-line two step search was about 8 times faster than an on-line one step search (for initial LIGO). In this paper we extend the two step search to the more realistic case of zero spin 1.5 post-Newtonian wave forms. We also present formulas for detection and false alarm probabilities which take statistical correlations into account. We find that for the case of a 1.5 post-Newtonian family of templates and signals, an on-line two step search requires about 1/21 the computing power that would be required for the corresponding on-line one step search. This reduction is achieved when signals having strength S = 10.34 are required to be detected with a probability of 0.95, at an average of one false event per year, and the noise power spectral density used is that of advanced LIGO. For initial LIGO, the reduction achieved in computing power is about 1/27 for S = 9.98 and the same probabilities for detection and false alarm as above.Comment: 30 page RevTeX file and 17 figures (postscript). Submitted to PRD Feb 21, 199

Fidelity amplitude of the scattering matrix in microwave cavities

The concept of fidelity decay is discussed from the point of view of the scattering matrix, and the scattering fidelity is introduced as the parametric cross-correlation of a given S-matrix element, taken in the time domain, normalized by the corresponding autocorrelation function. We show that for chaotic systems, this quantity represents the usual fidelity amplitude, if appropriate ensemble and/or energy averages are taken. We present a microwave experiment where the scattering fidelity is measured for an ensemble of chaotic systems. The results are in excellent agreement with random matrix theory for the standard fidelity amplitude. The only parameter, namely the perturbation strength could be determined independently from level dynamics of the system, thus providing a parameter free agreement between theory and experiment

On the Metric Dimension of Cartesian Products of Graphs

A set S of vertices in a graph G resolves G if every vertex is uniquely determined by its vector of distances to the vertices in S. The metric dimension of G is the minimum cardinality of a resolving set of G. This paper studies the metric dimension of cartesian products G*H. We prove that the metric dimension of G*G is tied in a strong sense to the minimum order of a so-called doubly resolving set in G. Using bounds on the order of doubly resolving sets, we establish bounds on G*H for many examples of G and H. One of our main results is a family of graphs G with bounded metric dimension for which the metric dimension of G*G is unbounded

Approximate Quantum Fourier Transform and Decoherence

We discuss the advantages of using the approximate quantum Fourier transform (AQFT) in algorithms which involve periodicity estimations. We analyse quantum networks performing AQFT in the presence of decoherence and show that extensive approximations can be made before the accuracy of AQFT (as compared with regular quantum Fourier transform) is compromised. We show that for some computations an approximation may imply a better performance.Comment: 14 pages, 10 fig. (8 *.eps files). More information on http://eve.physics.ox.ac.uk/QChome.html http://www.physics.helsinki.fi/~kasuomin http://www.physics.helsinki.fi/~kira/group.htm

Chronic y-secretase inhibition reduces amyloid plaque-associated instability of pre- and postsynaptic structures

The loss of synapses is a strong histological correlate of the cognitive decline in Alzheimer’s disease (AD). Amyloid bpeptide (Ab), a cleavage product of the amyloid precursor protein (APP), exerts detrimental effects on synapses, a process thought to be causally related to the cognitive deficits in AD. Here, we used in vivo two-photon microscopy to characterize the dynamics of axonal boutons and dendritic spines in APP/Presenilin 1 (APPswe/PS1L166P)–green fluorescent protein (GFP) transgenic mice. Time-lapse imaging over 4 weeks revealed a pronounced, concerted instability of pre- and postsynaptic structures within the vicinity of amyloid plaques. Treatment with a novel sulfonamide-type g-secretase inhibitor (GSI) attenuated the formation and growth of new plaques and, most importantly, led to a normalization of the enhanced dynamics of synaptic structures close to plaques. GSI treatment did neither affect spines and boutons distant from plaques in amyloid precursor protein/presenilin 1-GFP (APPPS1-GFP) nor those in GFP-control mice, suggesting no obvious neuropathological side effects of the drug

An integrated clinical program and crowdsourcing strategy for genomic sequencing and Mendelian disease gene discovery.

Despite major progress in defining the genetic basis of Mendelian disorders, the molecular etiology of many cases remains unknown. Patients with these undiagnosed disorders often have complex presentations and require treatment by multiple health care specialists. Here, we describe an integrated clinical diagnostic and research program using whole-exome and whole-genome sequencing (WES/WGS) for Mendelian disease gene discovery. This program employs specific case ascertainment parameters, a WES/WGS computational analysis pipeline that is optimized for Mendelian disease gene discovery with variant callers tuned to specific inheritance modes, an interdisciplinary crowdsourcing strategy for genomic sequence analysis, matchmaking for additional cases, and integration of the findings regarding gene causality with the clinical management plan. The interdisciplinary gene discovery team includes clinical, computational, and experimental biomedical specialists who interact to identify the genetic etiology of the disease, and when so warranted, to devise improved or novel treatments for affected patients. This program effectively integrates the clinical and research missions of an academic medical center and affords both diagnostic and therapeutic options for patients suffering from genetic disease. It may therefore be germane to other academic medical institutions engaged in implementing genomic medicine programs