science and technology

Bayes, Oracle Bayes and Empirical Bayes

Bradley Efron.

Source: Statistical Science, Volume 34, Number 2, 177--201.

Abstract:
This article concerns the Bayes and frequentist aspects of empirical Bayes inference. Some of the ideas explored go back to Robbins in the 1950s, while others are current. Several examples are discussed, real and artificial, illustrating the two faces of empirical Bayes methodology: “oracle Bayes” shows empirical Bayes in its most frequentist mode, while “finite Bayes inference” is a fundamentally Bayesian application. In either case, modern theory and computation allow us to present a sharp finite-sample picture of what is at stake in an empirical Bayes analysis.




science and technology

A Conversation with Dick Dudley

Vladimir Koltchinskii, Richard Nickl, Philippe Rigollet.

Source: Statistical Science, Volume 34, Number 1, 169--175.

Abstract:
Richard Mansfield Dudley (Dick Dudley) was born in 1938. He received the A.B. from Harvard in 1952 and the Ph.D. from Princeton in 1962 (under the supervision of Gilbert Hunt and Edward Nelson). Following an appointment at UC Berkeley as an assistant professor, he joined the Department of Mathematics at MIT in 1967. Dick Dudley has made fundamental contributions to the theory of Gaussian processes and Probability in Banach Spaces. Among his major achievements is the development of a general framework for empirical processes theory, in particular, for uniform central limit theorems. These results have had and continue having tremendous impact in contemporary statistics and in mathematical foundations of machine learning. A more extensive biographical sketch is contained in the preface to the Selected works of R. M. Dudley (editors: E. Giné, V. Koltchinskii and R. Norvaisa) published in 2010. This conversation took place (mostly, via email) in the fall of 2017.




science and technology

A Conversation with Piet Groeneboom

Geurt Jongbloed.

Source: Statistical Science, Volume 34, Number 1, 156--168.

Abstract:
Petrus (Piet) Groeneboom was born in Scheveningen in 1941 and grew up in Voorburg. Both villages are located near The Hague in The Netherlands; Scheveningen actually being part of The Hague. He attended the gymnasium of the Huygens lyceum. In 1959, he entered the University of Amsterdam, where he studied psychology. After his “candidate” exam (comparable to BSc) in 1963, he worked at the psychological laboratory of the University of Amsterdam until 1966. In 1965, he took up mathematics as a part-time study. After having obtained his master’s degree in 1971, he had a position at the psychological laboratory again until 1973, when he was appointed to the Mathematical Center in Amsterdam. There, he wrote between 1975 and 1979 his Ph.D. thesis with Kobus Oosterhoff as advisor, graduating in 1979. After a period of two years as visiting professor at the University of Washington (UW) in Seattle, Piet moved back to the Mathematical Center until he was appointed full professor of statistics at the University of Amsterdam in 1984. Four years later, he moved to Delft University of Technology where he became professor of statistics and stayed until his retirement in 2006. Between 2000 and 2006 he also held a part-time professorship at the Vrije Universiteit in Amsterdam. From 1999 till 2013 he was Affiliate Professor at the statistics department of UW, Seattle. Apart from being visiting professor at the UW in Seattle, he was also visiting professor at Stanford University, Université Paris 6 and ETH Zürich. Piet is well known for his work on shape constrained statistical inference. He worked on asymptotic theory for these problems, created algorithms to compute nonparametric estimates in such models and applied these models to real data. He also worked on interacting particle systems, extreme value analysis and efficiency theory for testing procedures. Piet (co-)authored four books and 64 papers and served as promotor of 13 students. He is the recipient of the 1985 Rollo Davidson prize, a fellow of the IMS and elected member of the ISI. In 2015, he delivered the Wald lecture at the Joint Statistical Meeting in Montreal. Piet and his wife Marijke live in Naarden. He has two sons, Thomas and Tim, and (since June 12, 2018) one grandson, Tarik. This conversation was held at Piet’s house in Naarden, on February 28 and April 24, 2018.




science and technology

Generalized Multiple Importance Sampling

Víctor Elvira, Luca Martino, David Luengo, Mónica F. Bugallo.

Source: Statistical Science, Volume 34, Number 1, 129--155.

Abstract:
Importance sampling (IS) methods are broadly used to approximate posterior distributions or their moments. In the standard IS approach, samples are drawn from a single proposal distribution and weighted adequately. However, since the performance in IS depends on the mismatch between the targeted and the proposal distributions, several proposal densities are often employed for the generation of samples. Under this multiple importance sampling (MIS) scenario, extensive literature has addressed the selection and adaptation of the proposal distributions, interpreting the sampling and weighting steps in different ways. In this paper, we establish a novel general framework with sampling and weighting procedures when more than one proposal is available. The new framework encompasses most relevant MIS schemes in the literature, and novel valid schemes appear naturally. All the MIS schemes are compared and ranked in terms of the variance of the associated estimators. Finally, we provide illustrative examples revealing that, even with a good choice of the proposal densities, a careful interpretation of the sampling and weighting procedures can make a significant difference in the performance of the method.




science and technology

Gaussian Integrals and Rice Series in Crossing Distributions—to Compute the Distribution of Maxima and Other Features of Gaussian Processes

Georg Lindgren.

Source: Statistical Science, Volume 34, Number 1, 100--128.

Abstract:
We describe and compare how methods based on the classical Rice’s formula for the expected number, and higher moments, of level crossings by a Gaussian process stand up to contemporary numerical methods to accurately deal with crossing related characteristics of the sample paths. We illustrate the relative merits in accuracy and computing time of the Rice moment methods and the exact numerical method, developed since the late 1990s, on three groups of distribution problems, the maximum over a finite interval and the waiting time to first crossing, the length of excursions over a level, and the joint period/amplitude of oscillations. We also treat the notoriously difficult problem of dependence between successive zero crossing distances. The exact solution has been known since at least 2000, but it has remained largely unnoticed outside the ocean science community. Extensive simulation studies illustrate the accuracy of the numerical methods. As a historical introduction an attempt is made to illustrate the relation between Rice’s original formulation and arguments and the exact numerical methods.




science and technology

Rejoinder: Response to Discussions and a Look Ahead

Vincent Dorie, Jennifer Hill, Uri Shalit, Marc Scott, Dan Cervone.

Source: Statistical Science, Volume 34, Number 1, 94--99.

Abstract:
Response to discussion of Dorie (2017), in which the authors of that piece express their gratitude to the discussants, rebut some specific criticisms, and argue that the limitations of the 2016 Atlantic Causal Inference Competition represent an exciting opportunity for future competitions in a similar mold.




science and technology

Comment: Contributions of Model Features to BART Causal Inference Performance Using ACIC 2016 Competition Data

Nicole Bohme Carnegie.

Source: Statistical Science, Volume 34, Number 1, 90--93.

Abstract:
With a thorough exposition of the methods and results of the 2016 Atlantic Causal Inference Competition, Dorie et al. have set a new standard for reproducibility and comparability of evaluations of causal inference methods. In particular, the open-source R package aciccomp2016, which permits reproduction of all datasets used in the competition, will be an invaluable resource for evaluation of future methodological developments. Building upon results from Dorie et al., we examine whether a set of potential modifications to Bayesian Additive Regression Trees (BART)—multiple chains in model fitting, using the propensity score as a covariate, targeted maximum likelihood estimation (TMLE), and computing symmetric confidence intervals—have a stronger impact on bias, RMSE, and confidence interval coverage in combination than they do alone. We find that bias in the estimate of SATT is minimal, regardless of the BART formulation. For purposes of CI coverage, however, all proposed modifications are beneficial—alone and in combination—but use of TMLE is least beneficial for coverage and results in considerably wider confidence intervals.




science and technology

Comment: Causal Inference Competitions: Where Should We Aim?

Ehud Karavani, Tal El-Hay, Yishai Shimoni, Chen Yanover.

Source: Statistical Science, Volume 34, Number 1, 86--89.

Abstract:
Data competitions proved to be highly beneficial to the field of machine learning, and thus expected to provide similar advantages in the field of causal inference. As participants in the 2016 and 2017 Atlantic Causal Inference Conference (ACIC) data competitions and co-organizers of the 2018 competition, we discuss the strengths of simulation-based competitions and suggest potential extensions to address their limitations. These suggested augmentations aim at making the data generating processes more realistic and gradually increase in complexity, allowing thorough investigations of algorithms’ performance. We further outline a community-wide competition framework to evaluate an end-to-end causal inference pipeline, beginning with a causal question and a database, and ending with causal estimates.




science and technology

Comment on “Automated Versus Do-It-Yourself Methods for Causal Inference: Lessons Learned from a Data Analysis Competition”

Susan Gruber, Mark J. van der Laan.

Source: Statistical Science, Volume 34, Number 1, 82--85.

Abstract:
Dorie and co-authors (DHSSC) are to be congratulated for initiating the ACIC Data Challenge. Their project engaged the community and accelerated research by providing a level playing field for comparing the performance of a priori specified algorithms. DHSSC identified themes concerning characteristics of the DGP, properties of the estimators, and inference. We discuss these themes in the context of targeted learning.




science and technology

Matching Methods for Causal Inference: A Review and a Look Forward

Elizabeth A. Stuart

Source: Statist. Sci., Volume 25, Number 1, 1--21.

Abstract:
When estimating causal effects using observational data, it is desirable to replicate a randomized experiment as closely as possible by obtaining treated and control groups with similar covariate distributions. This goal can often be achieved by choosing well-matched samples of the original treated and control groups, thereby reducing bias due to the covariates. Since the 1970s, work on matching methods has examined how to best choose treated and control subjects for comparison. Matching methods are gaining popularity in fields such as economics, epidemiology, medicine and political science. However, until now the literature and related advice has been scattered across disciplines. Researchers who are interested in using matching methods—or developing methods related to matching—do not have a single place to turn to learn about past and current research. This paper provides a structure for thinking about matching methods and guidance on their use, coalescing the existing research (both old and new) and providing a summary of where the literature on matching methods is now and where it should be headed.




science and technology

Heteromodal Cortical Areas Encode Sensory-Motor Features of Word Meaning

The capacity to process information in conceptual form is a fundamental aspect of human cognition, yet little is known about how this type of information is encoded in the brain. Although the role of sensory and motor cortical areas has been a focus of recent debate, neuroimaging studies of concept representation consistently implicate a network of heteromodal areas that seem to support concept retrieval in general rather than knowledge related to any particular sensory-motor content. We used predictive machine learning on fMRI data to investigate the hypothesis that cortical areas in this "general semantic network" (GSN) encode multimodal information derived from basic sensory-motor processes, possibly functioning as convergence–divergence zones for distributed concept representation. An encoding model based on five conceptual attributes directly related to sensory-motor experience (sound, color, shape, manipulability, and visual motion) was used to predict brain activation patterns associated with individual lexical concepts in a semantic decision task. When the analysis was restricted to voxels in the GSN, the model was able to identify the activation patterns corresponding to individual concrete concepts significantly above chance. In contrast, a model based on five perceptual attributes of the word form performed at chance level. This pattern was reversed when the analysis was restricted to areas involved in the perceptual analysis of written word forms. These results indicate that heteromodal areas involved in semantic processing encode information about the relative importance of different sensory-motor attributes of concepts, possibly by storing particular combinations of sensory and motor features.

SIGNIFICANCE STATEMENT The present study used a predictive encoding model of word semantics to decode conceptual information from neural activity in heteromodal cortical areas. The model is based on five sensory-motor attributes of word meaning (color, shape, sound, visual motion, and manipulability) and encodes the relative importance of each attribute to the meaning of a word. This is the first demonstration that heteromodal areas involved in semantic processing can discriminate between different concepts based on sensory-motor information alone. This finding indicates that the brain represents concepts as multimodal combinations of sensory and motor representations.




science and technology

The Joyful Reduction of Uncertainty: Music Perception as a Window to Predictive Neuronal Processing




science and technology

The Axon Initial Segment: An Updated Viewpoint

Christophe Leterrier
Feb 28, 2018; 38:2135-2145
Viewpoints




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Dopamine D1 and D2 Receptor Family Contributions to Modafinil-Induced Wakefulness

Jared W. Young
Mar 4, 2009; 29:2663-2665
Journal Club




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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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Multisensory Integration and the Society for Neuroscience: Then and Now

Barry E. Stein
Jan 2, 2020; 40:3-11
Viewpoints




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Optimization of a GCaMP Calcium Indicator for Neural Activity Imaging

Jasper Akerboom
Oct 3, 2012; 32:13819-13840
Cellular




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Metacognitive Mechanisms Underlying Lucid Dreaming

Elisa Filevich
Jan 21, 2015; 35:1082-1088
BehavioralSystemsCognitive




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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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The Cognitive Thalamus as a Gateway to Mental Representations

Mathieu Wolff
Jan 2, 2019; 39:3-14
Viewpoints




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Brain-Derived Neurotrophic Factor Protection of Cortical Neurons from Serum Withdrawal-Induced Apoptosis Is Inhibited by cAMP

Steven Poser
Jun 1, 2003; 23:4420-4427
Cellular




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The Next 50 Years of Neuroscience

Cara M. Altimus
Jan 2, 2020; 40:101-106
Viewpoints




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Physical Exercise Prevents Stress-Induced Activation of Granule Neurons and Enhances Local Inhibitory Mechanisms in the Dentate Gyrus

Timothy J. Schoenfeld
May 1, 2013; 33:7770-7777
BehavioralSystemsCognitive




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Genomic Analysis of Reactive Astrogliosis

Jennifer L. Zamanian
May 2, 2012; 32:6391-6410
Neurobiology of Disease




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Readiness Potential and Neuronal Determinism: New Insights on Libet Experiment

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




science and technology

Advances in Enteric Neurobiology: The "Brain" in the Gut in Health and Disease

Subhash Kulkarni
Oct 31, 2018; 38:9346-9354
Symposium and Mini-Symposium




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Sleep Deprivation Biases the Neural Mechanisms Underlying Economic Preferences

Vinod Venkatraman
Mar 9, 2011; 31:3712-3718
BehavioralSystemsCognitive




science and technology

Memory and Brain Systems: 1969-2009

Larry R. Squire
Oct 14, 2009; 29:12711-12716
40th Anniversary Retrospective




science and technology

Axonal ramifications of hippocampal Ca1 pyramidal cells

WD Knowles
Nov 1, 1981; 1:1236-1241
Articles




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Dissociable Intrinsic Connectivity Networks for Salience Processing and Executive Control

William W. Seeley
Feb 28, 2007; 27:2349-2356
BehavioralSystemsCognitive




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Microglia Actively Remodel Adult Hippocampal Neurogenesis through the Phagocytosis Secretome

Irune Diaz-Aparicio
Feb 12, 2020; 40:1453-1482
Development Plasticity Repair




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The Pain of Sleep Loss: A Brain Characterization in Humans

Adam J. Krause
Mar 20, 2019; 39:2291-2300
BehavioralSystemsCognitive




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{Delta}9-Tetrahydrocannabinol and Cannabinol Activate Capsaicin-Sensitive Sensory Nerves via a CB1 and CB2 Cannabinoid Receptor-Independent Mechanism

Peter M. Zygmunt
Jun 1, 2002; 22:4720-4727
Behavioral




science and technology

Afferents and Homotypic Neighbors Regulate Horizontal Cell Morphology, Connectivity, and Retinal Coverage

Benjamin E. Reese
Mar 2, 2005; 25:2167-2175
BehavioralSystemsCognitive




science and technology

Synaptic Specificity and Application of Anterograde Transsynaptic AAV for Probing Neural Circuitry

Brian Zingg
Apr 15, 2020; 40:3250-3267
Systems/Circuits




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Nurture versus Nature: Long-Term Impact of Forced Right-Handedness on Structure of Pericentral Cortex and Basal Ganglia

Stefan Klöppel
Mar 3, 2010; 30:3271-3275
BRIEF COMMUNICATION




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The Representation of Semantic Information Across Human Cerebral Cortex During Listening Versus Reading Is Invariant to Stimulus Modality

Fatma Deniz
Sep 25, 2019; 39:7722-7736
BehavioralSystemsCognitive




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Astrocytes Modulate Baroreflex Sensitivity at the Level of the Nucleus of the Solitary Tract

Svetlana Mastitskaya
Apr 8, 2020; 40:3052-3062
Systems/Circuits




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Daily Marijuana Use Is Not Associated with Brain Morphometric Measures in Adolescents or Adults

Barbara J. Weiland
Jan 28, 2015; 35:1505-1512
Neurobiology of Disease




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The Effect of Body Posture on Brain Glymphatic Transport

Hedok Lee
Aug 5, 2015; 35:11034-11044
Neurobiology of Disease




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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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Dural Calcitonin Gene-Related Peptide Produces Female-Specific Responses in Rodent Migraine Models

Amanda Avona
May 29, 2019; 39:4323-4331
Systems/Circuits




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Circuit Stability to Perturbations Reveals Hidden Variability in the Balance of Intrinsic and Synaptic Conductances

Sebastian Onasch
Apr 15, 2020; 40:3186-3202
Systems/Circuits




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Neurobiological Mechanisms of the Placebo Effect

Fabrizio Benedetti
Nov 9, 2005; 25:10390-10402
Symposia and Mini-Symposia




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Significant Neuroanatomical Variation Among Domestic Dog Breeds

Erin E. Hecht
Sep 25, 2019; 39:7748-7758
BehavioralSystemsCognitive




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Physiological Basis of Noise-Induced Hearing Loss in a Tympanal Ear

Ben Warren
Apr 8, 2020; 40:3130-3140
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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White Matter Microstructure in Transsexuals and Controls Investigated by Diffusion Tensor Imaging

Georg S. Kranz
Nov 12, 2014; 34:15466-15475
Systems/Circuits




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A Transcriptome Database for Astrocytes, Neurons, and Oligodendrocytes: A New Resource for Understanding Brain Development and Function

John D. Cahoy
Jan 2, 2008; 28:264-278
Cellular




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Grey Matter Volume Differences Associated with Extremely Low Levels of Cannabis Use in Adolescence

Catherine Orr
Mar 6, 2019; 39:1817-1827
BehavioralSystemsCognitive