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A hidden Markov model approach to characterizing the photo-switching behavior of fluorophores

Lekha Patel, Nils Gustafsson, Yu Lin, Raimund Ober, Ricardo Henriques, Edward Cohen.

Source: The Annals of Applied Statistics, Volume 13, Number 3, 1397--1429.

Abstract:
Fluorescing molecules (fluorophores) that stochastically switch between photon-emitting and dark states underpin some of the most celebrated advancements in super-resolution microscopy. While this stochastic behavior has been heavily exploited, full characterization of the underlying models can potentially drive forward further imaging methodologies. Under the assumption that fluorophores move between fluorescing and dark states as continuous time Markov processes, the goal is to use a sequence of images to select a model and estimate the transition rates. We use a hidden Markov model to relate the observed discrete time signal to the hidden continuous time process. With imaging involving several repeat exposures of the fluorophore, we show the observed signal depends on both the current and past states of the hidden process, producing emission probabilities that depend on the transition rate parameters to be estimated. To tackle this unusual coupling of the transition and emission probabilities, we conceive transmission (transition-emission) matrices that capture all dependencies of the model. We provide a scheme of computing these matrices and adapt the forward-backward algorithm to compute a likelihood which is readily optimized to provide rate estimates. When confronted with several model proposals, combining this procedure with the Bayesian Information Criterion provides accurate model selection.




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Noncommutative Lebesgue decomposition and contiguity with applications in quantum statistics

Akio Fujiwara, Koichi Yamagata.

Source: Bernoulli, Volume 26, Number 3, 2105--2142.

Abstract:
We herein develop a theory of contiguity in the quantum domain based upon a novel quantum analogue of the Lebesgue decomposition. The theory thus formulated is pertinent to the weak quantum local asymptotic normality introduced in the previous paper [Yamagata, Fujiwara, and Gill, Ann. Statist. 41 (2013) 2197–2217], yielding substantial enlargement of the scope of quantum statistics.




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On the best constant in the martingale version of Fefferman’s inequality

Adam Osękowski.

Source: Bernoulli, Volume 26, Number 3, 1912--1926.

Abstract:
Let $X=(X_{t})_{tgeq 0}in H^{1}$ and $Y=(Y_{t})_{tgeq 0}in{mathrm{BMO}} $ be arbitrary continuous-path martingales. The paper contains the proof of the inequality egin{equation*}mathbb{E}int _{0}^{infty }iglvert dlangle X,Y angle_{t}igrvert leq sqrt{2}Vert XVert _{H^{1}}Vert YVert _{mathrm{BMO}_{2}},end{equation*} and the constant $sqrt{2}$ is shown to be the best possible. The proof rests on the construction of a certain special function, enjoying appropriate size and concavity conditions.




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A fast algorithm with minimax optimal guarantees for topic models with an unknown number of topics

Xin Bing, Florentina Bunea, Marten Wegkamp.

Source: Bernoulli, Volume 26, Number 3, 1765--1796.

Abstract:
Topic models have become popular for the analysis of data that consists in a collection of n independent multinomial observations, with parameters $N_{i}inmathbb{N}$ and $Pi_{i}in[0,1]^{p}$ for $i=1,ldots,n$. The model links all cell probabilities, collected in a $p imes n$ matrix $Pi$, via the assumption that $Pi$ can be factorized as the product of two nonnegative matrices $Ain[0,1]^{p imes K}$ and $Win[0,1]^{K imes n}$. Topic models have been originally developed in text mining, when one browses through $n$ documents, based on a dictionary of $p$ words, and covering $K$ topics. In this terminology, the matrix $A$ is called the word-topic matrix, and is the main target of estimation. It can be viewed as a matrix of conditional probabilities, and it is uniquely defined, under appropriate separability assumptions, discussed in detail in this work. Notably, the unique $A$ is required to satisfy what is commonly known as the anchor word assumption, under which $A$ has an unknown number of rows respectively proportional to the canonical basis vectors in $mathbb{R}^{K}$. The indices of such rows are referred to as anchor words. Recent computationally feasible algorithms, with theoretical guarantees, utilize constructively this assumption by linking the estimation of the set of anchor words with that of estimating the $K$ vertices of a simplex. This crucial step in the estimation of $A$ requires $K$ to be known, and cannot be easily extended to the more realistic set-up when $K$ is unknown. This work takes a different view on anchor word estimation, and on the estimation of $A$. We propose a new method of estimation in topic models, that is not a variation on the existing simplex finding algorithms, and that estimates $K$ from the observed data. We derive new finite sample minimax lower bounds for the estimation of $A$, as well as new upper bounds for our proposed estimator. We describe the scenarios where our estimator is minimax adaptive. Our finite sample analysis is valid for any $n,N_{i},p$ and $K$, and both $p$ and $K$ are allowed to increase with $n$, a situation not handled well by previous analyses. We complement our theoretical results with a detailed simulation study. We illustrate that the new algorithm is faster and more accurate than the current ones, although we start out with a computational and theoretical disadvantage of not knowing the correct number of topics $K$, while we provide the competing methods with the correct value in our simulations.




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Local differential privacy: Elbow effect in optimal density estimation and adaptation over Besov ellipsoids

Cristina Butucea, Amandine Dubois, Martin Kroll, Adrien Saumard.

Source: Bernoulli, Volume 26, Number 3, 1727--1764.

Abstract:
We address the problem of non-parametric density estimation under the additional constraint that only privatised data are allowed to be published and available for inference. For this purpose, we adopt a recent generalisation of classical minimax theory to the framework of local $alpha$-differential privacy and provide a lower bound on the rate of convergence over Besov spaces $mathcal{B}^{s}_{pq}$ under mean integrated $mathbb{L}^{r}$-risk. This lower bound is deteriorated compared to the standard setup without privacy, and reveals a twofold elbow effect. In order to fulfill the privacy requirement, we suggest adding suitably scaled Laplace noise to empirical wavelet coefficients. Upper bounds within (at most) a logarithmic factor are derived under the assumption that $alpha$ stays bounded as $n$ increases: A linear but non-adaptive wavelet estimator is shown to attain the lower bound whenever $pgeq r$ but provides a slower rate of convergence otherwise. An adaptive non-linear wavelet estimator with appropriately chosen smoothing parameters and thresholding is shown to attain the lower bound within a logarithmic factor for all cases.




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Estimating the number of connected components in a graph via subgraph sampling

Jason M. Klusowski, Yihong Wu.

Source: Bernoulli, Volume 26, Number 3, 1635--1664.

Abstract:
Learning properties of large graphs from samples has been an important problem in statistical network analysis since the early work of Goodman ( Ann. Math. Stat. 20 (1949) 572–579) and Frank ( Scand. J. Stat. 5 (1978) 177–188). We revisit a problem formulated by Frank ( Scand. J. Stat. 5 (1978) 177–188) of estimating the number of connected components in a large graph based on the subgraph sampling model, in which we randomly sample a subset of the vertices and observe the induced subgraph. The key question is whether accurate estimation is achievable in the sublinear regime where only a vanishing fraction of the vertices are sampled. We show that it is impossible if the parent graph is allowed to contain high-degree vertices or long induced cycles. For the class of chordal graphs, where induced cycles of length four or above are forbidden, we characterize the optimal sample complexity within constant factors and construct linear-time estimators that provably achieve these bounds. This significantly expands the scope of previous results which have focused on unbiased estimators and special classes of graphs such as forests or cliques. Both the construction and the analysis of the proposed methodology rely on combinatorial properties of chordal graphs and identities of induced subgraph counts. They, in turn, also play a key role in proving minimax lower bounds based on construction of random instances of graphs with matching structures of small subgraphs.




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Reliable clustering of Bernoulli mixture models

Amir Najafi, Seyed Abolfazl Motahari, Hamid R. Rabiee.

Source: Bernoulli, Volume 26, Number 2, 1535--1559.

Abstract:
A Bernoulli Mixture Model (BMM) is a finite mixture of random binary vectors with independent dimensions. The problem of clustering BMM data arises in a variety of real-world applications, ranging from population genetics to activity analysis in social networks. In this paper, we analyze the clusterability of BMMs from a theoretical perspective, when the number of clusters is unknown. In particular, we stipulate a set of conditions on the sample complexity and dimension of the model in order to guarantee the Probably Approximately Correct (PAC)-clusterability of a dataset. To the best of our knowledge, these findings are the first non-asymptotic bounds on the sample complexity of learning or clustering BMMs.




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The Thomson family : fisherman in Buckhaven, retailers in Kapunda / compiled by Elizabeth Anne Howell.

Thomson (Family)




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From the coalfields of Somerset to the Adelaide Hills and beyond : the story of the Hewish Family : three centuries of one family's journey through time / Maureen Brown.

Hewish Henry -- Family.




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With a bottle of whisky in my hand : the family of James Grant and Isabella Masson / by Carolyn Cowgill.

Grant (Family)




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The Klemm family : descendants of Johann Gottfried Klemm and Anna Louise Klemm : these forebears are honoured and remembered at a reunion at Gruenberg, Moculta 11th-12th March 1995.

Klemm (Family)




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Hubbe family history items

Hubbe (Family)




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Geoff Nixon, man of the land : a history of Gunniguldrie and the Nixon family / Robert Nixon.

Nixon, Geoffrey Owen, 1921-2011.




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Item 02: William Hilton Saunders WWI diary, 1 January 1917 - 24 October 1917




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Item 03: William Hilton Saunders WWI diary, 1 January 1918 - 31 December 1918




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Willie Neville Majoribank Chester manuscript collection, 5 November 1915 - 22 December 1918




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Item 2: George Hugh Morrison diary, 1 January 1917-9 October 1917




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Item 02: Captain Vernon Sturdee diary, 3 September, 1915- 31 December, 1915




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Item 03: Captain Vernon Sturdee diary, 22 September, 1915- 23 January, 1916




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Letter from J. H Bannatyne to Other Windsor Berry Esq. relating to the Myall Creek Massacre, 17 December 1838




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Item 01: Notebooks (2) containing hand written copies of 123 letters from Major William Alan Audsley to his parents, ca. 1916-ca. 1919, transcribed by his father. Also includes original letters (2) written by Major Audsley.




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Item 01: Scorebook of the Aboriginal Cricket Tour of England being a copy in Charles Lawrence's hand, 1868




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Item 01: Autograph letter signed, from Hume, Appin, to William E. Riley, concerning an account for money owed by Riley, 4 September 1834




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Smart research for HSC students: Better searching with online resources

In this online session, we simplify searching for you so that the skills you need in one resource will work wherever you are.




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Russia probe transcripts released by House Intelligence Committee

Reaction and analysis from Fox News contributor Byron York and former Florida Attorney General Pam Bondi.





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Federal watchdog finds 'reasonable grounds to believe' vaccine doctor's ouster was retaliation, lawyers say

The Office of Special Counsel is recommending that ousted vaccine official Dr. Rick Bright be reinstated while it investigates his case, his lawyers announced Friday.Bright while leading coronavirus vaccine development was recently removed from his position as the director of the Department of Health and Human Services' Biomedical Advanced Research and Development Authority, and he alleges it was because he insisted congressional funding not go toward "drugs, vaccines, and other technologies that lack scientific merit" and limited the "broad use" of hydroxychloroquine after it was touted by President Trump. In a whistleblower complaint, he alleged "cronyism" at HHS. He has also alleged he was "pressured to ignore or dismiss expert scientific recommendations and instead to award lucrative contracts based on political connections."On Friday, Bright's lawyers said that the Office of Special Counsel has determined there are "reasonable grounds to believe" his firing was retaliation, The New York Times reports. The federal watchdog also recommended he be reinstated for 45 days to give the office "sufficient time to complete its investigation of Bright's allegations," CNN reports. The decision on whether to do so falls on Secretary of Health and Human Services Alex Azar, and Office of Special Counsel recommendations are "not binding," the Times notes. More stories from theweek.com Outed CIA agent Valerie Plame is running for Congress, and her launch video looks like a spy movie trailer 7 scathing cartoons about America's rush to reopen Trump says he couldn't have exposed WWII vets to COVID-19 because the wind was blowing the wrong way





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'We Cannot Police Our Way Out of a Pandemic.' Experts, Police Union Say NYPD Should Not Be Enforcing Social Distance Rules Amid COVID-19

The New York City police department (NYPD) is conducting an internal investigation into a May 2 incident involving the violent arrests of multiple people, allegedly members of a group who were not social distancing





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The McMichaels can't be charged with a hate crime by the state in the shooting death of Ahmaud Arbery because the law doesn't exist in Georgia

Georgia is one of four states that doesn't have a hate crime law. Arbery's killing has reignited calls for legislation.





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Nearly one-third of Americans believe a coronavirus vaccine exists and is being withheld, survey finds

The Democracy Fund + UCLA Nationscape Project found some misinformation about the coronavirus is more widespread that you might think.





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Neighbor of father and son arrested in Ahmaud Arbery killing is also under investigation

The ongoing investigation of the fatal shooting in Brunswick, Georgia, will also look at a neighbor of suspects Gregory and Travis McMichael who recorded video of the incident, authorities said.





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Beyond Whittle: Nonparametric Correction of a Parametric Likelihood with a Focus on Bayesian Time Series Analysis

Claudia Kirch, Matthew C. Edwards, Alexander Meier, Renate Meyer.

Source: Bayesian Analysis, Volume 14, Number 4, 1037--1073.

Abstract:
Nonparametric Bayesian inference has seen a rapid growth over the last decade but only few nonparametric Bayesian approaches to time series analysis have been developed. Most existing approaches use Whittle’s likelihood for Bayesian modelling of the spectral density as the main nonparametric characteristic of stationary time series. It is known that the loss of efficiency using Whittle’s likelihood can be substantial. On the other hand, parametric methods are more powerful than nonparametric methods if the observed time series is close to the considered model class but fail if the model is misspecified. Therefore, we suggest a nonparametric correction of a parametric likelihood that takes advantage of the efficiency of parametric models while mitigating sensitivities through a nonparametric amendment. We use a nonparametric Bernstein polynomial prior on the spectral density with weights induced by a Dirichlet process and prove posterior consistency for Gaussian stationary time series. Bayesian posterior computations are implemented via an MH-within-Gibbs sampler and the performance of the nonparametrically corrected likelihood for Gaussian time series is illustrated in a simulation study and in three astronomy applications, including estimating the spectral density of gravitational wave data from the Advanced Laser Interferometer Gravitational-wave Observatory (LIGO).




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Comment: Models as (Deliberate) Approximations

David Whitney, Ali Shojaie, Marco Carone.

Source: Statistical Science, Volume 34, Number 4, 591--598.




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Comment: “Models as Approximations I: Consequences Illustrated with Linear Regression” by A. Buja, R. Berk, L. Brown, E. George, E. Pitkin, L. Zhan and K. Zhang

Roderick J. Little.

Source: Statistical Science, Volume 34, Number 4, 580--583.




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A Conversation with Robert E. Kass

Sam Behseta.

Source: Statistical Science, Volume 34, Number 2, 334--348.

Abstract:
Rob Kass has been been on the faculty of the Department of Statistics at Carnegie Mellon since 1981; he joined the Center for the Neural Basis of Cognition (CNBC) in 1997, and the Machine Learning Department (in the School of Computer Science) in 2007. He served as Department Head of Statistics from 1995 to 2004 and served as Interim Co-Director of the CNBC 2015–2018. He became the Maurice Falk Professor of Statistics and Computational Neuroscience in 2016. Kass has served as Chair of the Section for Bayesian Statistical Science of the American Statistical Association, Chair of the Statistics Section of the American Association for the Advancement of Science, founding Editor-in-Chief of the journal Bayesian Analysis and Executive Editor of Statistical Science . He is an elected Fellow of the American Statistical Association, the Institute of Mathematical Statistics and the American Association for the Advancement of Science. He has been recognized by the Institute for Scientific Information as one of the 10 most highly cited researchers, 1995–2005, in the category of mathematics. Kass is the recipient of the 2017 Fisher Award and lectureship by the Committee of the Presidents of the Statistical Societies. This interview took place at Carnegie Mellon University in November 2017.




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The Importance of Being Clustered: Uncluttering the Trends of Statistics from 1970 to 2015

Laura Anderlucci, Angela Montanari, Cinzia Viroli.

Source: Statistical Science, Volume 34, Number 2, 280--300.

Abstract:
In this paper, we retrace the recent history of statistics by analyzing all the papers published in five prestigious statistical journals since 1970, namely: The Annals of Statistics , Biometrika , Journal of the American Statistical Association , Journal of the Royal Statistical Society, Series B and Statistical Science . The aim is to construct a kind of “taxonomy” of the statistical papers by organizing and clustering them in main themes. In this sense being identified in a cluster means being important enough to be uncluttered in the vast and interconnected world of the statistical research. Since the main statistical research topics naturally born, evolve or die during time, we will also develop a dynamic clustering strategy, where a group in a time period is allowed to migrate or to merge into different groups in the following one. Results show that statistics is a very dynamic and evolving science, stimulated by the rise of new research questions and types of data.




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Be nice to yourself and others / design : Biman Mullick.

London : Cleanair, Smoke-free Environment (33 Stillness Rd, London, SE23 1NG), [198-?]




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Be nice to yourself and others / design : Biman Mullick.

London : Cleanair, Smoke-free Environment (33 Stillness Rd, London, SE23 1NG), [198-?]




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How can the smoker and the nonsmoker be equally free in the same place? George Bernard Shaw / Biman Mullick.

[London?], [199-?]




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Danny Smith from No Human Being Is Illegal (in all our glory). Collaged photograph by Deborah Kelly and collaborators, 2014-2018.

[London], 2019.




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Taylor Swift, Hailey Bieber, and Tons of Other Celebs’ Favorite Leggings Are on Sale Ahead of Black Friday

Here’s where you can snag their Alo Yoga Moto leggings for less.




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These Nordstrom Cyber Monday Deals Are Giving Black Friday a Run for Its Money

This is not a drill: You can get up to 50% off at Nordstrom right now.




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Macy’s Insane Cyber Monday Sale Ends in a Few Hours—Here Are the Best Deals

You've got exactly four hours left to take advantage of these heavily discounted prices.




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Sweatsuits Should Be Your Cozy Day Uniform—and These Are Our Favorites From Amazon

This retro style is making a comeback for a reason.




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This is the Only Jacket I’ll Be Living in This Winter

Canada Goose has long been a leader in the outdoor gear space.




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Allometric Analysis Detects Brain Size-Independent Effects of Sex and Sex Chromosome Complement on Human Cerebellar Organization

Catherine Mankiw
May 24, 2017; 37:5221-5231
Development Plasticity Repair




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Gut Microbes and the Brain: Paradigm Shift in Neuroscience

Emeran A. Mayer
Nov 12, 2014; 34:15490-15496
Symposium




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Readiness Potential and Neuronal Determinism: New Insights on Libet Experiment

Karim Fifel
Jan 24, 2018; 38:784-786
Journal Club




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Fingolimod Rescues Demyelination in a Mouse Model of Krabbe's Disease

Sibylle Béchet
Apr 8, 2020; 40:3104-3118
Neurobiology of Disease




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Where Is the Anterior Temporal Lobe and What Does It Do?

Michael F. Bonner
Mar 6, 2013; 33:4213-4215
Journal Club




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Brain Structures Differ between Musicians and Non-Musicians

Christian Gaser
Oct 8, 2003; 23:9240-9245
BehavioralSystemsCognitive