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Contrastive Similarity Matching for Supervised Learning.

Neural Comput 2021 Feb 22:1-29. Epub 2021 Feb 22.

John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA 02138, U.S.A.

We propose a novel biologically plausible solution to the credit assignment problem motivated by observations in the ventral visual pathway and trained deep neural networks. In both, representations of objects in the same category become progressively more similar, while objects belonging to different categories become less similar. We use this observation to motivate a layer-specific learning goal in a deep network: each layer aims to learn a representational similarity matrix that interpolates between previous and later layers. Read More

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February 2021

Quantum Flags and New Bounds on the Quantum Capacity of the Depolarizing Channel.

Phys Rev Lett 2020 Jul;125(2):020503

NEST, Scuola Normale Superiore and Istituto Nanoscienze-CNR, I-56126 Pisa, Italy.

A new upper bound for the quantum capacity of the d-dimensional depolarizing channels is presented. Our derivation makes use of a flagged extension of the map where the receiver obtains a copy of a state σ_{0} whenever the messages are transmitted without errors, and a copy of a state σ_{1}, when instead the original state gets fully depolarized. By varying the overlap between the flag states, the resulting transformation nicely interpolates between the depolarizing map (when σ_{0}=σ_{1}), and the d-dimensional erasure channel (when σ_{0} and σ_{1} have orthogonal support). Read More

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Coadapted genomes and selection on hybrids: Fisher's geometric model explains a variety of empirical patterns.

Evol Lett 2018 Oct 14;2(5):472-498. Epub 2018 Aug 14.

Department of Genetics University of Cambridge Downing St. Cambridge CB23EH United Kingdom.

Natural selection plays a variety of roles in hybridization, speciation, and admixture. Most research has focused on two extreme cases: crosses between closely related inbred lines, where hybrids are fitter than their parents, or crosses between effectively isolated species, where hybrids suffer severe breakdown. But many natural populations must fall into intermediate regimes, with multiple types of gene interaction, and these are more difficult to study. Read More

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October 2018

How proteins modify water dynamics.

J Chem Phys 2018 Jun;148(21):215103

Division of Biophysical Chemistry, Department of Chemistry, Lund University, P.O. Box 124, SE-22100 Lund, Sweden.

Much of biology happens at the protein-water interface, so all dynamical processes in this region are of fundamental importance. Local structural fluctuations in the hydration layer can be probed by O magnetic relaxation dispersion (MRD), which, at high frequencies, measures the integral of a biaxial rotational time correlation function (TCF)-the integral rotational correlation time. Numerous O MRD studies have demonstrated that this correlation time, when averaged over the first hydration shell, is longer than in bulk water by a factor 3-5. Read More

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Full-Body Locomotion Reconstruction of Virtual Characters Using a Single Inertial Measurement Unit.

Christos Mousas

Sensors (Basel) 2017 Nov 10;17(11). Epub 2017 Nov 10.

Department of Computer Science, Southern Illinois University, 1230 Lincoln Drive, Mail Code 4511, Carbondale, IL 62901, USA.

This paper presents a method of reconstructing full-body locomotion sequences for virtual characters in real-time, using data from a single inertial measurement unit (IMU). This process can be characterized by its difficulty because of the need to reconstruct a high number of degrees of freedom (DOFs) from a very low number of DOFs. To solve such a complex problem, the presented method is divided into several steps. Read More

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November 2017

Probability distributions for directed polymers in random media with correlated noise.

Phys Rev E 2016 Jul 1;94(1-1):010101. Epub 2016 Jul 1.

Department of Physics, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA.

The probability distribution for the free energy of directed polymers in random media (DPRM) with uncorrelated noise in d=1+1 dimensions satisfies the Tracy-Widom distribution. We inquire if and how this universal distribution is modified in the presence of spatially correlated noise. The width of the distribution scales as the DPRM length to an exponent β, in good (but not full) agreement with previous renormalization group and numerical results. Read More

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The spin and orbital contributions to the total magnetic moments of free Fe, Co, and Ni clusters.

J Chem Phys 2015 Sep;143(10):104302

Institut für Experimentalphysik, Universität Hamburg, Luruper Chausee 149, 22761 Hamburg, Germany.

We present size dependent spin and orbital magnetic moments of cobalt (Con (+), 8 ≤ n ≤ 22), iron (Fen (+), 7 ≤ n ≤ 17), and nickel cluster (Nin (+), 7 ≤ n ≤ 17) cations as obtained by X-ray magnetic circular dichroism (XMCD) spectroscopy of isolated clusters in the gas phase. The spin and orbital magnetic moments range between the corresponding atomic and bulk values in all three cases. We compare our findings to previous XMCD data, Stern-Gerlach data, and computational results. Read More

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September 2015

Phonon contribution to the entropy of hard-sphere crystals.

Veit Elser

Phys Rev E Stat Nonlin Soft Matter Phys 2014 May 19;89(5):052404. Epub 2014 May 19.

Department of Physics, Cornell University, Ithaca, New York, USA.

Comparing the entropies of hard spheres in the limit of close packing, for different stacking sequences of the hexagonal layers, has been a challenge because the differences are so small. Here we present a method based on a "sticky-sphere" model by which the system interpolates between hard spheres in one limit and a harmonic crystal in the other. For the fcc and hcp stackings we have calculated the entropy difference in the harmonic (sticky) limit, as well as the differences in the free energy change upon removing the stickiness in the model. Read More

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MRI upsampling using feature-based nonlocal means approach.

IEEE Trans Med Imaging 2014 Oct 12;33(10):1969-85. Epub 2014 Jun 12.

In magnetic resonance imaging (MRI), spatial resolution is limited by several factors such as acquisition time, short physiological phenomena, and organ motion. The acquired image usually has higher resolution in two dimensions (the acquisition plane) in comparison with the third dimension, resulting in highly anisotropic voxel size. Interpolation of these low resolution (LR) images using standard techniques, such as linear or spline interpolation, results in distorted edges in the planes perpendicular to the acquisition plane. Read More

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October 2014

Landscape scale estimation of soil carbon stock using 3D modelling.

Sci Total Environ 2014 Jul 11;487:578-86. Epub 2014 Mar 11.

Cranfield University, Bldg. 37, School of Applied Sciences, MK43 0AL Bedfordshire, United Kingdom.

Soil C is the largest pool of carbon in the terrestrial biosphere, and yet the processes of C accumulation, transformation and loss are poorly accounted for. This, in part, is due to the fact that soil C is not uniformly distributed through the soil depth profile and most current landscape level predictions of C do not adequately account the vertical distribution of soil C. In this study, we apply a method based on simple soil specific depth functions to map the soil C stock in three-dimensions at landscape scale. Read More

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Heterogeneous aspirations promote cooperation in the prisoner's dilemma game.

PLoS One 2010 Dec 6;5(12):e15117. Epub 2010 Dec 6.

Faculty of Natural Sciences and Mathematics, University of Maribor, Slovenia.

To be the fittest is central to proliferation in evolutionary games. Individuals thus adopt the strategies of better performing players in the hope of successful reproduction. In structured populations the array of those that are eligible to act as strategy sources is bounded to the immediate neighbors of each individual. Read More

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December 2010

Connectivity, dynamics, and memory in reservoir computing with binary and analog neurons.

Neural Comput 2010 May;22(5):1272-311

Institute for Theoretical Computer Science, Graz University of Technology, Graz, Austria.

Reservoir computing (RC) systems are powerful models for online computations on input sequences. They consist of a memoryless readout neuron that is trained on top of a randomly connected recurrent neural network. RC systems are commonly used in two flavors: with analog or binary (spiking) neurons in the recurrent circuits. Read More

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Exact results for the Barabási queuing model.

C Anteneodo

Phys Rev E Stat Nonlin Soft Matter Phys 2009 Oct 27;80(4 Pt 1):041131. Epub 2009 Oct 27.

Departamento de Física, PUC-Rio and National Institute of Science and Technology for Complex Systems, Rua Marquês de São Vicente 225, CEP 22453-900 Rio de Janeiro, Brazil.

Previous works on the queuing model introduced by Barabási to account for the heavy tailed distributions of the temporal patterns found in many human activities mainly concentrate on the extremal dynamics case and on lists of only two items. Here we obtain exact results for the general case with arbitrary values of the list length L and of the degree of randomness that interpolates between the deterministic and purely random limits. The statistically fundamental quantities are extracted from the solution of master equations. Read More

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October 2009

Surface Reconstruction From Non-parallel Curve Networks.


Comput Graph Forum 2008 Apr;27(2):155-163

Building surfaces from cross-section curves has wide applications including bio-medical modeling. Previous work in this area has mostly focused on connecting simple closed curves on parallel cross-sections. Here we consider the more general problem where input data may lie on non-parallel cross-sections and consist of curve networks that represent the segmentation of the underlying object by different material or tissue types (e. Read More

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Generic mixed columnar-plaquette phases in Rokhsar-Kivelson models.

Phys Rev Lett 2008 Jan 22;100(3):037201. Epub 2008 Jan 22.

Laboratoire de Physique Théorique, Centre National de la Recherche Scientifique and Université de Toulouse, Toulouse, France.

We revisit the phase diagram of Rokhsar-Kivelson models, which are used in fields such as superconductivity, frustrated magnetism, cold bosons, and the physics of Josephson junction arrays. From an extended height effective theory, we show that one of two simple generic phase diagrams contains a mixed phase that interpolates continuously between columnar and plaquette states. For the square lattice quantum dimer model we present evidence from exact diagonalization and Green's function Monte Carlo techniques that this scenario is realized, by combining an analysis of the excitation gaps of different symmetry sectors with information on plaquette structure factors. Read More

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January 2008

Full-frame video stabilization with motion inpainting.

IEEE Trans Pattern Anal Mach Intell 2006 Jul;28(7):1150-63

Microsoft Research Asia, 3/F, Beijing Sigma Center, No. 49, Zhichun Road, Hai Dian District, Beijing, China 100080.

Video stabilization is an important video enhancement technology which aims at removing annoying shaky motion from videos. We propose a practical and robust approach of video stabilization that produces full-frame stabilized videos with good visual quality. While most previous methods end up with producing smaller size stabilized videos, our completion method can produce full-frame videos by naturally filling in missing image parts by locally aligning image data of neighboring frames. Read More

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Electrophoretic mobility of rigid rodlike particles in dilute aqueous and glycerol suspensions: comparison between theory and experiment.

J Colloid Interface Sci 2002 Jul;251(1):208-13

Department of Chemical Engineering, Cornell University, 120 Olin Hall, Ithaca, New York, 14853, USA.

The electrophoretic mobilities of rigid rodlike tobacco mosaic virus (TMV) particles solvated in water and in 80% glycerol/20% water solutions with a wide range of electrical double-layer thicknesses have been measured by Deggelmann et al. (Deggelmann, M., Graf, C. Read More

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The interpolation of object and surface structure.

Cogn Psychol 2002 Mar;44(2):148-90

Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge 02139, USA.

One of the main theoretical challenges of vision science is to explain how the visual system interpolates missing structure. Two forms of visual completion have been distinguished on the basis of the phenomenological states that they induce. Modal completion refers to the formation of visible surfaces and/or contours in image regions where these properties are not specified locally. Read More

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Derivation of protein-specific pair potentials based on weak sequence fragment similarity.

Proteins 2000 Jan;38(1):3-16

Laboratory of Computational Genomics, Danforth Plant Science Center, St. Louis, Missouri 63108, USA.

A method is presented for the derivation of knowledge-based pair potentials that corrects for the various compositions of different proteins. The resulting statistical pair potential is more specific than that derived from previous approaches as assessed by gapless threading results. Additionally, a methodology is presented that interpolates between statistical potentials when no homologous examples to the protein of interest are in the structural database used to derive the potential, to a Go-like potential (in which native interactions are favorable and all nonnative interactions are not) when homologous proteins are present. Read More

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January 2000
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