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Contrast Invariant SNR and Isotonic Regressions

Pierre Weiss, Paul Escande, Gabriel Bathie, Yiqiu Dong
2019 International Journal of Computer Vision  
This problem can be expressed as an isotonic regression problem.  ...  We design an image quality measure independent of contrast changes, which are defined as a set of transformations preserving an order between the level lines of an image.  ...  of (7) and SN R glo (u 1 , u 0 ) = −10 log 10 (∆ glo (u 1 , u 0 )/ u 0 2 2 ) denote the globally contrast invariant SNR.  ... 
doi:10.1007/s11263-019-01161-9 fatcat:kzomlxadnjasfjfwzqpgjohp7e

On Automatic Absorption Detection for Imaging Spectroscopy: A Comparative Study

Zhouyu Fu, Antonio Robles-Kelly, Terry Caelli, Robby T. Tan
2007 IEEE Transactions on Geoscience and Remote Sensing  
In addition to these methods, we also present a novel absorption recovery approach based upon unimodal regression and continuum removal.  ...  We commence by viewing the algorithms in the literature from a technical perspective and presenting an overview of the derivative analysis, Fingerprint and Maximum Modulus Wavelet Transform (MMWT) techniques  ...  Mainbourg, who kindly provided them with the implementation of the MMWT and the Fingerprint method used in the experimental section of this paper.  ... 
doi:10.1109/tgrs.2007.903402 fatcat:vdxliuv3qnfnxo2ckqth4gpuoy

Chemoenvironmental modulators of fluidity in the suspended biological cell

John M. Maloney, Krystyn J. Van Vliet
2014 Soft Matter  
The fluidity (mechanical hysteresivity) of cells in suspension is altered strongly by temperature, actin depolymerization, and osmotic swelling.  ...  Acknowledgments This work was supported by the Singapore-MIT Alliance for Research and Technology (SMART) Centre (BioSyM IRG). We gratefully acknowledge guidance from J. Guck  ...  Amplitudes and phase angles were extracted from deformation signals by subtracting a moving average across one or more periods and fitting the expression F sin[ω(t − t 0 ) − φ] by nonlinear regression  ... 
doi:10.1039/c4sm00743c pmid:25160132 fatcat:c4cgckmvibfzbke42t4rsu5wou

Effects of miRNA-15 and miRNA-16 expression replacement in chronic lymphocytic leukemia: implication for therapy

G Cutrona, S Matis, M Colombo, C Massucco, G Baio, F Valdora, L Emionite, S Fabris, A G Recchia, M Gentile, C E Neumaier, D Reverberi (+15 others)
2017 Leukemia  
Administration of miRNA mimics to NSG mice previously engrafted with CLL 51 clones resulted in substantial tumor regression.  ...  We 44 have investigated the effects of replacement of miR-15a and miR-16-1.  ...  In contrast, mice treated with miR-15 or miR-16 mimics showed a 332 significant ΔSNR% decrease (P<0.0001 and P=0.0002, respectively) compared to mice before 333 therapy administration (Figure 3c).  ... 
doi:10.1038/leu.2016.394 pmid:28053325 fatcat:ifuneucb4ne6vbd5iiudwvtxka

Quantitative Magnetic Particle Imaging Monitors the Transplantation, Biodistribution, and Clearance of Stem Cells In Vivo

Bo Zheng, Marc P. von See, Elaine Yu, Beliz Gunel, Kuan Lu, Tandis Vazin, David V. Schaffer, Patrick W. Goodwill, Steven M. Conolly
2016 Theranostics  
MPI offers near-ideal image contrast, depth penetration, and robustness; these properties make MPI both ultra-sensitive and linearly quantitative.  ...  taken up by liver and spleen.  ...  Acknowledgments The authors would like to thank Paul Keselman and Dr. Mike Wendland for MRI and CT assistance, and Analytical Resources Incorporated for ICP analysis.  ... 
doi:10.7150/thno.13728 pmid:26909106 pmcid:PMC4737718 fatcat:5p6nefhf25dkhlsumjaphyrcau

Automated assessment of prosody production

Jan P.H. van Santen, Emily Tucker Prud'hommeaux, Lois M. Black
2009 Speech Communication  
The judges identified the prosodic categories of the two utterances and rated the strength of their contrast.  ...  Speech was analyzed from children in six tasks designed to elicit specific prosodic contrasts.  ...  on an earlier draft of the paper, in particular on the LSR section; Rhea Paul for helpful comments on an earlier draft of the paper and for suggesting the Lexical van Santen et al.  ... 
doi:10.1016/j.specom.2009.04.007 pmid:20160984 pmcid:PMC2753987 fatcat:eq35jciuovcpzlbejyd2witjsy

On Stein's lemma, dependent covariates and functional monotonicity in multi-dimensional modeling

Chunming Zhang, Jialiang Li, Jingci Meng
2008 Journal of Multivariate Analysis  
Gaussian, and independent non-Gaussian.  ...  The simplicity and effectiveness of the proposed method are illustrated via simulation studies and real data application.  ...  According to Theorem 2, we would expect to find an isotonic increasing regression function of Y = ln(wage) in X 1 as well as in X 2 .  ... 
doi:10.1016/j.jmva.2008.02.018 fatcat:4prjfge6qfgyjd2kjimgxvlatm

Conditional analysis for mixed covariates, with application to feed intake of lactating sows [article]

So Young Park, Cai Li, Santa-Maria Mendoza, Eric van Heugten, and Ana-Maria Staicu
2019 arXiv   pre-print
The methodology accommodates flexible model structure, allows for joint estimation of the quantiles at all levels, and involves a computationally efficient estimation algorithm.  ...  The methodology is motivated by and applied to a lactating sow study, where the primary interest is to understand how the dynamic change of minute-by-minute temperature in the farrowing rooms within a  ...  Acknowledgement Staicu's research was supported partially by National Science Foundation DMS 0454942 and National Institutes of Health grants R01 NS085211 and R01 MH086633.  ... 
arXiv:1605.05779v2 fatcat:mqkyudwuizdotlqpr67ykovjdq

On the Nonasymptotic Convergence of Cyclic Coordinate Descent Methods

Ankan Saha, Ambuj Tewari
2013 SIAM Journal on Optimization  
We fill this gap in the literature by proving O(1/k) convergence rates (where k is the iteration count) for two variants of cyclic coordinate descent under an isotonicity assumption.  ...  Cyclic coordinate descent is a classic optimization method that has witnessed a resurgence of interest in Signal Processing, Statistics, and Machine Learning.  ...  The coefficient α is chosen so that the signal to noise ratio (SNR) is 3.0.  ... 
doi:10.1137/110840054 fatcat:6gdd4bjg6zhkbl2qc3ybxtgf2e

Relative changes of cerebral arterial and venous blood volumes during increased cerebral blood flow: Implications for BOLD fMRI

Sang-Pil Lee, Timothy Q. Duong, Guang Yang, Costantino Iadecola, Seong-Gi Kim
2001 Magnetic Resonance in Medicine  
Our findings provide a quantitative physiological model of BOLD contrast. Magn Reson Med 45:791-800, 2001.  ...  In particular, the change in venous blood volume induced by neural activity is one critical component of the blood oxygenation level-dependent (BOLD) signal because BOLD contrast is dependent only on venous  ...  Marlene Richter, Hellmut Merkle, and Gregor Adriany for hardware support, and Eric Cohen for proofreading the manuscript.  ... 
doi:10.1002/mrm.1107 pmid:11323805 fatcat:ljexsow3srb3fkfkw4simdwogm

Fast online deconvolution of calcium imaging data

Johannes Friedrich, Pengcheng Zhou, Liam Paninski, Joshua Vogelstein
2017 PLoS Computational Biology  
Our algorithm is a generalization of the pool adjacent violators algorithm (PAVA) for isotonic regression and inherits its linear-time computational complexity.  ...  We thank John Cunningham and Eftychios Pnevmatikakis for helpful conversations as well as Scott Linderman and Daniel Soudry for valuable comments on the manuscript.  ...  Acknowledgments We would like to thank Misha Ahrens and Yu Mu for providing whole-brain imaging data of larval zebrafish.  ... 
doi:10.1371/journal.pcbi.1005423 pmid:28291787 pmcid:PMC5370160 fatcat:tgwetfqbiffgpkhep2bzu3sqdu

Blind sparse deconvolution for inferring spike trains from fluorescence recordings [article]

Jérôme Tubiana, Sébastien Wolf, Georges Debregeas
2017 bioRxiv   pre-print
Furthermore, we provide solutions for the practical problems of thresholding and determination of the rise and decay time constants.  ...  We demonstrate that this method outperforms existing sparse deconvolution algorithms in terms of robustness, speed and/or accuracy on both synthetic and real fluorescence data.  ...  In [14] , the authors apply the Pool-Adjascent Violator Algorithm originally developed for isotonic regression problems to solve this optimization in an even faster yet greedy way. II.  ... 
doi:10.1101/156364 fatcat:rmjpthbounhafpn4uhfe3dn6sm

Multiscale methods for data on graphs and irregular multidimensional situations

Maarten Jansen, Guy P. Nason, B. W. Silverman
2009 Journal of The Royal Statistical Society Series B-statistical Methodology  
We demonstrate that our methods perform very well when compared to several other methods for spatial regression for both real and simulated data.  ...  Although our article concentrates on multiscale shrinkage (regression) we present our new 'wavelet transforms' as generic tools intended to be the basis of methods that might benefit from a multiscale  ...  Acknowledgements The authors would like to thank Cathy Goss and Inigo Everson of the British Antarctic Survey for supplying them with the krill data and for helpful conversations and advice concerning  ... 
doi:10.1111/j.1467-9868.2008.00672.x fatcat:ucpsnmalajbdxghldfvtaupyki

Hyperbolic Wavelet-Fisz Denoising for a Model Arising in Ultrasound Imaging

Younes Farouj, Jean-Marc Freyermuth, Laurent Navarro, Marianne Clausel, Philippe Delachartre
2017 IEEE Transactions on Computational Imaging  
The data-driven extension removes the need for any prior knowledge of the noise model parameters by estimating the noise variance using an isotonic Nadaraya-Watson estimator.  ...  Experiments on synthetic and real data, and comparisons with other noise reduction methods demonstrate the potential of our method at recovering ultrasound images while preserving tissue details.  ...  This can be done using the so-called isotonic regression, which consists in finding the closest non-decreasing function, in term of least mean square error, using a "pool-adjacent-violators" algorithm  ... 
doi:10.1109/tci.2016.2625740 fatcat:ghplxuqmpzb3rlh42sdxmqpi74

Community-based benchmarking improves spike rate inference from two-photon calcium imaging data [article]

Philipp Berens, Jeremy Freeman, Thomas Deneux, Nicolay Chenkov, Thomas McColgan, Artur Speiser, Jakob H. Macke, Srinivas Turaga, Patrick Mineault, Peter Rupprecht, Stephan Gerhard, Rainer W. Friedrich (+17 others)
2017 bioRxiv   pre-print
In recent years, two-photon calcium imaging has become a standard tool to probe the function of neural circuits and to study computations in neuronal populations.  ...  Acknowledgements This work was funded by the German Ministry of Education and Research (BMBF;  ...  Statistical inference under order restrictions: The theory and application of isotonic regression (Wiley New York, 1972). 30. Pachitariu, M., Stringer, C. & Harris, K. D.  ... 
doi:10.1101/177956 fatcat:erw3vyi6mbfllinzgbkaognuvi
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