Stan : A Probabilistic Programming Language

Carpenter, Bob; Gelman, Andrew; Hoffman, Matthew D.; Lee, Daniel; Goodrich, Ben; Betancourt, Michael; Brubaker, Marcus; Guo, Jiqiang; Li, Peter; Riddell, Allen

doi:10.18637/jss.v076.i01

Title: Stan : A Probabilistic Programming Language

Journal Article · Sun Jan 01 00:00:00 EST 2017 · Journal of Statistical Software

DOI:https://doi.org/10.18637/jss.v076.i01· OSTI ID:1430202

Carpenter, Bob ^[1]; Gelman, Andrew ^[1]; Hoffman, Matthew D. ^[2]; Lee, Daniel ^[1]; Goodrich, Ben ^[1]; Betancourt, Michael ^[1]; Brubaker, Marcus ^[3]; Guo, Jiqiang ^[4]; Li, Peter ^[1]; Riddell, Allen ^[5]

Columbia Univ., New York, NY (United States)
Adobe Creative Intelligence Lab, San Jose, CA (United States)
York Univ., Toronto (Canada)
NPD Group, Inc., Port Washington, NY (United States)
Indiana Univ., Bloomington, IN (United States)

Stan is a probabilistic programming language for specifying statistical models. A Stan program imperatively defines a log probability function over parameters conditioned on specified data and constants. As of version 2.14.0, Stan provides full Bayesian inference for continuous-variable models through Markov chain Monte Carlo methods such as the No-U-Turn sampler, an adaptive form of Hamiltonian Monte Carlo sampling. Penalized maximum likelihood estimates are calculated using optimization methods such as the limited memory Broyden-Fletcher-Goldfarb-Shanno algorithm. Stan is also a platform for computing log densities and their gradients and Hessians, which can be used in alternative algorithms such as variational Bayes, expectation propagation, and marginal inference using approximate integration. To this end, Stan is set up so that the densities, gradients, and Hessians, along with intermediate quantities of the algorithm such as acceptance probabilities, are easily accessible. Stan can also be called from the command line using the cmdstan package, through R using the rstan package, and through Python using the pystan package. All three interfaces support sampling and optimization-based inference with diagnostics and posterior analysis. rstan and pystan also provide access to log probabilities, gradients, Hessians, parameter transforms, and specialized plotting.

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Research Organization:: Columbia Univ., New York, NY (United States); Harvard Univ., Cambridge, MA (United States)

Sponsoring Organization:: USDOE; National Science Foundation (NSF); US Dept. of Education, Inst. of Education Sciences (IES); National Institutes of Health (NIH)

Grant/Contract Number:: SC0002099; ATM-0934516; ED-GRANTS-032309-005; R305D090006-09A; 1G20RR030893-01; CNS-1205516

OSTI ID:: 1430202

Journal Information:: Journal of Statistical Software, Vol. 76, Issue 1; ISSN 1548-7660

Country of Publication:: United States

Language:: English

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Cited by: 2444 works

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Timing of maternal exposure to toxic cyanobacteria and offspring fitness in Daphnia magna : Implications for the evolution of anticipatory maternal effects Radersma, Reinder; Hegg, Alexander; Noble, Daniel W. A. Ecology and Evolution, Vol. 8, Issue 24 https://doi.org/10.1002/ece3.4700	journal	November 2018
Identifying occupancy model inadequacies: can residuals separately assess detection and presence? Wright, Wilson J.; Irvine, Kathryn M.; Higgs, Megan D. Ecology https://doi.org/10.1002/ecy.2703	journal	April 2019
Spatial correlations of ground motion for non‐ergodic seismic hazard analysis Kuehn, Nicolas M.; Abrahamson, Norman A. Earthquake Engineering & Structural Dynamics, Vol. 49, Issue 1 https://doi.org/10.1002/eqe.3221	journal	October 2019
Latency of tobacco smoking for head and neck cancer among HPV‐positive and HPV‐negative individuals Madathil, Sreenath; Rousseau, Marie‐Claude; Joseph, Lawrence International Journal of Cancer, Vol. 147, Issue 1 https://doi.org/10.1002/ijc.32708	journal	October 2019
Efficient inference of generalized spatial fusion models with flexible specification Wang, Craig; Furrer, Reinhard Stat, Vol. 8, Issue 1 https://doi.org/10.1002/sta4.216	journal	January 2019
Formal Specification for Deep Neural Networks Seshia, Sanjit A.; Desai, Ankush; Dreossi, Tommaso Automated Technology for Verification and Analysis https://doi.org/10.1007/978-3-030-01090-4_2	book	January 2018
A Hierarchical Ornstein-Uhlenbeck Model for Stochastic Time Series Analysis Laitinen, Ville; Lahti, Leo Advances in Intelligent Data Analysis XVII https://doi.org/10.1007/978-3-030-01768-2_16	book	October 2018
Reparametrizing the Sigmoid Model of Gene Regulation for Bayesian Inference Modrák, Martin Computational Methods in Systems Biology https://doi.org/10.1007/978-3-319-99429-1_20	book	January 2018
Bayesian bivariate subgroup analysis for risk–benefit evaluation Henderson, Nicholas C.; Varadhan, Ravi Health Services and Outcomes Research Methodology, Vol. 18, Issue 4 https://doi.org/10.1007/s10742-018-0188-1	journal	October 2018
Population pharmacokinetic reanalysis of a Diazepam PBPK model: a comparison of Stan and GNU MCSim Tsiros, Periklis; Bois, Frederic Y.; Dokoumetzidis, Aristides Journal of Pharmacokinetics and Pharmacodynamics, Vol. 46, Issue 2 https://doi.org/10.1007/s10928-019-09630-x	journal	April 2019
X vs. Y: an analysis of intergenerational differences in transport mode use among young adults Krueger, Rico; Rashidi, Taha H.; Vij, Akshay Transportation, Vol. 47, Issue 5 https://doi.org/10.1007/s11116-019-10009-7	journal	May 2019
When Your Robot Avatar Misbehaves You Are Likely to Apologize: An Exploration of Guilt During Robot Embodiment Aymerich-Franch, Laura; Kishore, Sameer; Slater, Mel International Journal of Social Robotics, Vol. 12, Issue 1 https://doi.org/10.1007/s12369-019-00556-5	journal	May 2019
Understanding the Stochastic Partial Differential Equation Approach to Smoothing Miller, David L.; Glennie, Richard; Seaton, Andrew E. Journal of Agricultural, Biological and Environmental Statistics, Vol. 25, Issue 1 https://doi.org/10.1007/s13253-019-00377-z	journal	September 2019
Environmental Exposure Mixtures: Questions and Methods to Address Them Hamra, Ghassan B.; Buckley, Jessie P. Current Epidemiology Reports, Vol. 5, Issue 2 https://doi.org/10.1007/s40471-018-0145-0	journal	April 2018
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The Value of Empirical Data for Estimating the Parameters of a Sociohydrological Flood Risk Model Barendrecht, M. H.; Viglione, A.; Kreibich, H. Water Resources Research, Vol. 55, Issue 2 https://doi.org/10.1029/2018WR024128	journal	February 2019
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Quantifying climate sensitivity and climate-driven change in North American amphibian communities Miller, David A. W.; Grant, Evan H. Campbell; Muths, Erin Nature Communications, Vol. 9, Issue 1 https://doi.org/10.1038/s41467-018-06157-6	journal	September 2018
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Forecasting at Scale Taylor, Sean J.; Letham, Benjamin The American Statistician, Vol. 72, Issue 1 https://doi.org/10.1080/00031305.2017.1380080	journal	January 2018
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Linking regional shifts in microbial genome adaptation with surface ocean biogeochemistry Garcia, Catherine A.; Hagstrom, George I.; Larkin, Alyse A. Philosophical Transactions of the Royal Society B: Biological Sciences, Vol. 375, Issue 1798 https://doi.org/10.1098/rstb.2019.0254	journal	March 2020
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Identifying Model-Based and Model-Free Patterns in Behavior on Multi-Step Tasks Miller, Kevin J.; Brody, Carlos D.; Botvinick, Matthew M. https://doi.org/10.1101/096339	posted_content	December 2016
Inferring continuous and discrete population genetic structure across space Bradburd, Gideon S.; Coop, Graham M.; Ralph, Peter L. https://doi.org/10.1101/189688	posted_content	September 2017
Transcranial alternating current stimulation at 10 Hz modulates response bias in the Somatic Signal Detection Task Craddock, Matt; Klepousniotou, Ekaterini; el-Deredy, Wael https://doi.org/10.1101/330134	posted_content	May 2018
Orienting to Polarized Light at Night—Matching Lunar Skylight to Performance in a Nocturnal Beetle Foster, James J.; Kirwan, John D.; el Jundi, Basil https://doi.org/10.1101/366583	posted_content	November 2018
Intraspecific variation in Artiodactyla social organisation: A Bayesian phylogenetic multilevel analysis of detailed population-level data Miles, M. I.; Jaeggi, A. V.; Festa-Bianchet, M. https://doi.org/10.1101/603399	posted_content	April 2019
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Environment affects specialisation of plants and pollinators Cagua, E. Fernando; Lustig, Audrey; Tylianakis, Jason M. bioRxiv https://doi.org/10.1101/866772	posted_content	December 2019
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Measuring competitive impact: Joint‐species modelling of invaded plant communities O’Reilly‐Nugent, Andrew; Wandrag, Elizabeth M.; Catford, Jane A. Journal of Ecology https://doi.org/10.1111/1365-2745.13280	journal	October 2019
Dirichlet‐multinomial modelling outperforms alternatives for analysis of microbiome and other ecological count data Harrison, Joshua G.; Calder, W. John; Shastry, Vivaswat Molecular Ecology Resources, Vol. 20, Issue 2 https://doi.org/10.1111/1755-0998.13128	journal	January 2020
Bayesian inference and simulation approaches improve the assessment of Elo‐ratings in the analysis of social behaviour Goffe, Adeelia S.; Fischer, Julia; Sennhenn‐Reulen, Holger Methods in Ecology and Evolution, Vol. 9, Issue 10 https://doi.org/10.1111/2041-210x.13072	journal	July 2018
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Neural hierarchical models of ecological populations Joseph, Maxwell B. Ecology Letters, Vol. 23, Issue 4 https://doi.org/10.1111/ele.13462	journal	April 2020
Relating beta diversity of birds and butterflies in the Great Basin to spatial resolution, environmental variables and trait-based groups Yen, Jian D. L.; Fleishman, Erica; Fogarty, Frank Global Ecology and Biogeography, Vol. 28, Issue 3 https://doi.org/10.1111/geb.12852	journal	December 2018
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Identification of multiple distinct neurogenic motor patterns that can occur simultaneously in the guinea pig distal colon Costa, Marcello; Keightley, Lauren J.; Wiklendt, Lukasz American Journal of Physiology-Gastrointestinal and Liver Physiology, Vol. 316, Issue 1 https://doi.org/10.1152/ajpgi.00256.2018	journal	January 2019
Great Equalizer or Great Selector? Reconsidering Education as a Moderator of Intergenerational Transmissions Fiel, Jeremy E. Sociology of Education, Vol. 93, Issue 4 https://doi.org/10.1177/0038040720927886	journal	June 2020
Criminogenic Factors Associated with Noncompliance and Rearrest of Mental Health Court Participants Honegger, Laura N.; Honegger, Kyle S. Criminal Justice and Behavior, Vol. 46, Issue 9 https://doi.org/10.1177/0093854819862010	journal	June 2019
Quantifying performance of a diagnostic test as the expected information for discrimination: Relation to the C -statistic McKeigue, Paul Statistical Methods in Medical Research, Vol. 28, Issue 6 https://doi.org/10.1177/0962280218776989	journal	July 2018
Estimation of delay to diagnosis and incidence in HIV using indirect evidence of infection dates Stirrup, Oliver T.; Dunn, David T. BMC Medical Research Methodology, Vol. 18, Issue 1 https://doi.org/10.1186/s12874-018-0522-x	journal	June 2018
How pupil responses track value-based decision-making during and after reinforcement learning Van Slooten, Joanne C.; Jahfari, Sara; Knapen, Tomas PLOS Computational Biology, Vol. 14, Issue 11 https://doi.org/10.1371/journal.pcbi.1006632	journal	November 2018
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Computational modelling reveals contrasting effects on reinforcement learning and cognitive flexibility in stimulant use disorder and obsessive-compulsive disorder: remediating effects of dopaminergic D2/3 receptor agents Kanen, Jonathan W.; Ersche, Karen D.; Fineberg, Naomi A. Apollo - University of Cambridge Repository https://doi.org/10.17863/cam.55231	text	January 2019
Impairments in reinforcement learning do not explain enhanced habit formation in cocaine use disorder Lim, T. V.; Cardinal, R. N.; Savulich, G. Apollo - University of Cambridge Repository https://doi.org/10.17863/cam.55729	text	January 2019
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Designing Robust N-of-1 Studies for Precision Medicine: Simulation Study and Design Recommendations Percha, Bethany; Baskerville, Edward B.; Johnson, Matthew Journal of Medical Internet Research, Vol. 21, Issue 4 https://doi.org/10.2196/12641	journal	January 2019
Indices of Effect Existence and Significance in the Bayesian Framework Makowski, Dominique; Ben-Shachar, Mattan S.; Chen, S. H. Annabel https://doi.org/10.31234/osf.io/2zexr	preprint	December 2019
Accounting for Bacterial Overlap Between Raw Water Communities and Contaminating Sources Improves the Accuracy of Signature-Based Microbial Source Tracking Hägglund, Moa; Bäckman, Stina; Macellaro, Anna Frontiers in Microbiology, Vol. 9 https://doi.org/10.3389/fmicb.2018.02364	journal	October 2018
The relative merit of empirical priors in non-identifiable and sloppy models: Applications to models of learning and decision-making: Empirical priors Spektor, Mikhail S.; Kellen, David Psychonomic Bulletin & Review, Vol. 25, Issue 6 https://doi.org/10.3758/s13423-018-1446-5	journal	March 2018
The Carnegie Supernova Project: Absolute Calibration and the Hubble Constant Burns, Christopher R.; Parent, Emilie; Phillips, M. M. The Astrophysical Journal, Vol. 869, Issue 1 https://doi.org/10.3847/1538-4357/aae51c	journal	December 2018
Choosing priors in bayesian measurement invariance modeling: A Monte Carlo Simulation study Pokropek, Artur; Schmidt, Peter; Davidov, Eldad Taylor & Francis https://doi.org/10.5167/uzh-182461	text	January 2020
The Impact of Moderate Priors For Bayesian Estimation and Testing of Item Factor Analysis Models When Maximum Likelihood is Unsuitable Bainter, Sierra A.; Forster, Daniel E. Taylor & Francis https://doi.org/10.6084/m9.figshare.6960449	text	January 2018
DeepPoseKit, a software toolkit for fast and robust animal pose estimation using deep learning Graving, Jacob M.; Chae, Daniel; Naik, Hemal eLife, Vol. 8 https://doi.org/10.7554/eLife.47994	journal	October 2019
Switch rates do not influence weighting of rare events in decisions from experience, but optional stopping does Soo, Kevin W.; Rottman, Benjamin M. Journal of Behavioral Decision Making, Vol. 31, Issue 5 https://doi.org/10.1002/bdm.2080	journal	April 2018
Site fertility drives temporal turnover of vegetation at high latitudes Maliniemi, Tuija; Happonen, Konsta; Virtanen, Risto Ecology and Evolution, Vol. 9, Issue 23 https://doi.org/10.1002/ece3.5778	journal	October 2019
Predictive probability of success using surrogate endpoints Saint‐Hilary, Gaelle; Barboux, Valentine; Pannaux, Matthieu Statistics in Medicine, Vol. 38, Issue 10 https://doi.org/10.1002/sim.8060	journal	December 2018
Heterogeneity of treatment effect of prophylactic pantoprazole in adult ICU patients: a post hoc analysis of the SUP-ICU trial Granholm, Anders; Marker, Søren; Krag, Mette Intensive Care Medicine, Vol. 46, Issue 4 https://doi.org/10.1007/s00134-019-05903-8	journal	January 2020
Interdependent effects of climate variability and forest cover change on streamflow dynamics: a case study in the Upper Umvoti River Basin, South Africa Lebek, Karen; Senf, Cornelius; Frantz, David Regional Environmental Change, Vol. 19, Issue 7 https://doi.org/10.1007/s10113-019-01521-8	journal	July 2019
Towards Bayesian hierarchical inference of equilibrium climate sensitivity from a combination of CMIP5 climate models and observational data Jonko, Alexandra; Urban, Nathan M.; Nadiga, Balu Climatic Change, Vol. 149, Issue 2 https://doi.org/10.1007/s10584-018-2232-0	journal	July 2018
Multivariate outlier detection in medicare claims payments applying probabilistic programming methods Bauder, Richard A.; Khoshgoftaar, Taghi M. Health Services and Outcomes Research Methodology, Vol. 17, Issue 3-4 https://doi.org/10.1007/s10742-017-0172-1	journal	June 2017
Prediction of tool-wear in turning of medical grade cobalt chromium molybdenum alloy (ASTM F75) using non-parametric Bayesian models McParland, Damien; Baron, Szymon; O’Rourke, Sarah Journal of Intelligent Manufacturing, Vol. 30, Issue 3 https://doi.org/10.1007/s10845-017-1317-3	journal	March 2017
Extending Bayesian back-calculation to estimate age and time specific HIV incidence Brizzi, Francesco; Birrell, Paul J.; Plummer, Martyn T. Lifetime Data Analysis, Vol. 25, Issue 4 https://doi.org/10.1007/s10985-019-09465-1	journal	February 2019
Root volume distribution of maturing perennial grasses revealed by correcting for minirhizotron surface effects Black, Christopher K.; Masters, Michael D.; LeBauer, David S. Plant and Soil, Vol. 419, Issue 1-2 https://doi.org/10.1007/s11104-017-3333-7	journal	July 2017
Robust Bayesian model selection for variable clustering with the Gaussian graphical model Andrade, Daniel; Takeda, Akiko; Fukumizu, Kenji Statistics and Computing https://doi.org/10.1007/s11222-019-09879-9	journal	July 2019
Modeling the Relationship between Water Level, Wild Rice Abundance, and Waterfowl Abundance at a Central North American Wetland Aagaard, Kevin; Eash, Josh; Ford, Walt Wetlands, Vol. 39, Issue 1 https://doi.org/10.1007/s13157-018-1025-6	journal	April 2018
On the Applicability of Probabilistic Programming Languages for Causal Activity Recognition Lüdtke, Stefan; Popko, Maximilian; Kirste, Thomas KI - Künstliche Intelligenz, Vol. 33, Issue 4 https://doi.org/10.1007/s13218-019-00580-7	journal	April 2019
The effect of thinning on mechanical properties of Douglas fir, Norway spruce, and Sitka spruce Krajnc, Luka; Farrelly, Niall; Harte, Annette M. Annals of Forest Science, Vol. 76, Issue 1 https://doi.org/10.1007/s13595-018-0787-6	journal	January 2019
Variational Bayesian inference for the multiple-choice DINA model Yamaguchi, Kazuhiro Behaviormetrika, Vol. 47, Issue 1 https://doi.org/10.1007/s41237-020-00104-w	journal	January 2020
Religious belief and cognitive conflict sensitivity: A preregistered fMRI study Hoogeveen, Suzanne; Snoek, Lukas; van Elk, Michiel Cortex, Vol. 129 https://doi.org/10.1016/j.cortex.2020.04.011	journal	August 2020
Bayesian Calibration of the Mg/Ca Paleothermometer in Planktic Foraminifera Tierney, Jessica E.; Malevich, Steven B.; Gray, William Paleoceanography and Paleoclimatology, Vol. 34, Issue 12 https://doi.org/10.1029/2019pa003744	journal	December 2019
Therapeutic reduction of ataxin-2 extends lifespan and reduces pathology in TDP-43 mice Becker, Lindsay A.; Huang, Brenda; Bieri, Gregor Nature, Vol. 544, Issue 7650 https://doi.org/10.1038/nature22038	journal	April 2017
Nutrient supply controls particulate elemental concentrations and ratios in the low latitude eastern Indian Ocean Garcia, Catherine A.; Baer, Steven E.; Garcia, Nathan S. Nature Communications, Vol. 9, Issue 1 https://doi.org/10.1038/s41467-018-06892-w	journal	November 2018
Positive reward prediction errors during decision-making strengthen memory encoding Jang, Anthony I.; Nassar, Matthew R.; Dillon, Daniel G. Nature Human Behaviour, Vol. 3, Issue 7 https://doi.org/10.1038/s41562-019-0597-3	journal	May 2019
Direct Evidence of Adult Aedes albopictus Dispersal by Car Eritja, Roger; Palmer, John R. B.; Roiz, David Scientific Reports, Vol. 7, Issue 1 https://doi.org/10.1038/s41598-017-12652-5	journal	October 2017
Integrated targeted metabolomic and lipidomic analysis: A novel approach to classifying early cystic precursors to invasive pancreatic cancer Gaiser, Rogier Aäron; Pessia, Alberto; Ateeb, Zeeshan Scientific Reports, Vol. 9, Issue 1 https://doi.org/10.1038/s41598-019-46634-6	journal	July 2019
Feature engineering applied to intraoperative in vivo Raman spectroscopy sheds light on molecular processes in brain cancer: a retrospective study of 65 patients Lemoine, Émile; Dallaire, Frédérick; Yadav, Rajeev The Analyst, Vol. 144, Issue 22 https://doi.org/10.1039/c9an01144g	journal	January 2019
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A mathematical model of cocoa bean fermentation Moreno-Zambrano, Mauricio; Grimbs, Sergio; Ullrich, Matthias S. Royal Society Open Science, Vol. 5, Issue 10 https://doi.org/10.1098/rsos.180964	journal	October 2018
Accounting for individual-specific variation in habitat-selection studies: Efficient estimation of mixed-effects models using Bayesian or frequentist computation Muff, Stefanie; Signer, Johannes; Fieberg, John bioRxiv https://doi.org/10.1101/411801	posted_content	January 2019
Birds invest wingbeats to keep a steady head and reap the ultimate benefits of flocking Taylor, Lucy A.; Biro, Dora; Lambert, Ben https://doi.org/10.1101/492090	posted_content	December 2018
Comparing and Validating Automated Tools for Individualized Electric Field Simulations in the Human Head Puonti, Oula; Saturnino, Guilherme B.; Madsen, Kristoffer H. https://doi.org/10.1101/611962	posted_content	April 2019
Impact of age-specific immunity on the timing and burden of the next Zika virus outbreak Counotte, Michel J.; Althaus, Christian L.; Low, Nicola https://doi.org/10.1101/661223	posted_content	July 2019
Reconstruction of plant–pollinator networks from observational data Young, Jean-Gabriel; Valdovinos, Fernanda S.; Newman, M. E. J. https://doi.org/10.1101/754077	posted_content	June 2021
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A global synthesis reveals biodiversity-mediated benefits for crop production Dainese, Matteo; Martin, Emily A.; Aizen, Marcelo A. Science Advances, Vol. 5, Issue 10 https://doi.org/10.1126/sciadv.aax0121	journal	October 2019
Association of response to TNF inhibitors in rheumatoid arthritis with quantitative trait loci for CD40 and CD39 Spiliopoulou, Athina; Colombo, Marco; Plant, Darren Annals of the Rheumatic Diseases, Vol. 78, Issue 8 https://doi.org/10.1136/annrheumdis-2018-214877	journal	April 2019
Bayesian Approaches to Assessing the Parallel Lines Assumption in Cumulative Ordered Logit Models Xu, Jun; Bauldry, Shawn G.; Fullerton, Andrew S. Sociological Methods & Research https://doi.org/10.1177/0049124119882461	journal	November 2019
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An engineered human Fc domain that behaves like a pH-toggle switch for ultra-long circulation persistence Lee, Chang-Han; Kang, Tae Hyun; Godon, Ophélie Nature Communications, Vol. 10, Issue 1 https://doi.org/10.1038/s41467-019-13108-2	journal	November 2019
Soil properties explain tree growth and mortality, but not biomass, across phosphorus-depleted tropical forests Soong, Jennifer L.; Janssens, Ivan A.; Grau, Oriol Scientific Reports, Vol. 10, Issue 1 https://doi.org/10.1038/s41598-020-58913-8	journal	February 2020
Applying causal models to explore the mechanism of action of simvastatin in progressive multiple sclerosis Eshaghi, Arman; Kievit, Rogier A.; Prados, Ferran Proceedings of the National Academy of Sciences, Vol. 116, Issue 22 https://doi.org/10.1073/pnas.1818978116	journal	May 2019
Scoring Depression on a Common Metric: A Comparison of EAP Estimation, Plausible Value Imputation, and Full Bayesian IRT Modeling Fischer, H. Felix; Rose, Matthias Multivariate Behavioral Research, Vol. 54, Issue 1 https://doi.org/10.1080/00273171.2018.1491381	journal	September 2018
Restraint and Critical Incident Reduction Following Introduction of the Neurosequential Model of Therapeutics (NMT) Hambrick, Erin P.; Brawner, Thomas W.; Perry, Bruce D. Residential Treatment for Children & Youth, Vol. 35, Issue 1 https://doi.org/10.1080/0886571x.2018.1425651	journal	January 2018
Genomic Perspective on Multivariate Variation, Pleiotropy, and Evolution Melo, Diogo; Marroig, Gabriel; Wolf, Jason B. Journal of Heredity, Vol. 110, Issue 4 https://doi.org/10.1093/jhered/esz011	journal	April 2019
Herbarium specimens reveal substantial and unexpected variation in phenological sensitivity across the eastern United States Park, Daniel S.; Breckheimer, Ian; Williams, Alex C. Philosophical Transactions of the Royal Society B: Biological Sciences, Vol. 374, Issue 1763 https://doi.org/10.1098/rstb.2017.0394	journal	November 2018
Pseudotime estimation: deconfounding single cell time series Reid, John; Wernisch, Lorenz Bioinformatics https://doi.org/10.1101/019588	journal	May 2015
Artificial Intelligence for Ecological and Evolutionary Synthesis Desjardins-Proulx, Philippe; Poisit, Timothee; Gravel, Dominique Frontiers in Ecology and Evolution https://doi.org/10.1101/161125	journal	September 2019
Accurate and simultaneous identification of differential expression and splicing using hierarchical Bayesian analysis Karlebach, Guy; Hansen, Peter; Veiga, Diogo F. T. Genome Biology https://doi.org/10.1101/2019.12.16.878884	journal	December 2019
The functional organization of high-level visual cortex determines the representation of complex visual stimuli Kliger, Libi; Yovel, Galit The Journal of Neuroscience https://doi.org/10.1101/2019.12.22.852293	journal	December 2019
Value Representations in the Orbitofrontal Cortex Drive Learning, not Choice Miller, Kevin J.; Botvinick, Matthew M.; Brody, Carlos D. eLife https://doi.org/10.1101/245720	journal	July 2022
Translation elongation and mRNA stability are coupled through the ribosomal A-site Hanson, Gavin; Alhusaini, Najwa; Morris, Nathan RNA https://doi.org/10.1101/300467	journal	April 2018
Spatial variation in exploited metapopulations obscures risk of collapse Okamoto, Daniel K.; Hessing-Lewis, Margot; Samhouri, Jameal F. Ecological Applications https://doi.org/10.1101/315481	journal	October 2019
Bayesian Hypothesis Testing And Experimental Design For Two-Photon Imaging Data Rogerson, Luke E.; Zhao, Zhijian; Franke, Katrin PLOS Computational Biology https://doi.org/10.1101/410357	journal	September 2018
Untangling the dynamics of persistence and colonization in microbial communities Ranjeva, Sylvia L.; Mihaljevic, Joseph R.; Joseph, Maxwell B. The ISME Journal https://doi.org/10.1101/427542	journal	April 2019
souporcell: Robust clustering of single cell RNAseq by genotype and ambient RNA inference without reference genotypes Heaton, Haynes; Talman, Arthur M.; Knights, Andrew BioRxiv https://doi.org/10.1101/699637	posted_content	September 2019
Anxious and obsessive-compulsive traits are independently associated with valuation of non-instrumental information Bennett, Daniel; Sutcliffe, Kiran; Tan, Nicholas Poh-Jie Journal of Experimental Psychology: General https://doi.org/10.1101/768168	journal	May 2020
Tunings for leapfrog integration of Hamiltonian Monte Carlo for estimating genetic parameters Arakawa, Aisaku; Hayashi, Takeshi; Taniguchi, Masaaki BioRxiv https://doi.org/10.1101/805499	posted_content	October 2019
Accounting for individual‐specific variation in habitat‐selection studies: Efficient estimation of mixed‐effects models using Bayesian or frequentist computation Muff, Stefanie; Signer, Johannes; Fieberg, John Journal of Animal Ecology, Vol. 89, Issue 1 https://doi.org/10.1111/1365-2656.13087	journal	September 2019
Diverse knowledge systems reveal social–ecological dynamics that inform species conservation status Lee, Lynn Chi; Thorley, Joe; Watson, Jane Conservation Letters, Vol. 12, Issue 2 https://doi.org/10.1111/conl.12613	journal	October 2018
Metapopulation dynamics in a changing climate: Increasing spatial synchrony in weather conditions drives metapopulation synchrony of a butterfly inhabiting a fragmented landscape Kahilainen, Aapo; van Nouhuys, Saskya; Schulz, Torsti Global Change Biology, Vol. 24, Issue 9 https://doi.org/10.1111/gcb.14280	journal	May 2018
Continuation of emtricitabine/lamivudine within combination antiretroviral therapy following detection of the M184V/I HIV‐1 resistance mutation Stirrup, Ot; Asboe, D.; Pozniak, A. HIV Medicine, Vol. 21, Issue 5 https://doi.org/10.1111/hiv.12829	journal	January 2020
Trace types and denotational semantics for sound programmable inference in probabilistic languages Lew, Alexander K.; Cusumano-Towner, Marco F.; Sherman, Benjamin Proceedings of the ACM on Programming Languages, Vol. 4, Issue POPL https://doi.org/10.1145/3371087	journal	January 2020
Implicit Gender Bias in Linguistic Descriptions for Expected Events: The Cases of the 2016 United States and 2017 United Kingdom Elections von der Malsburg, Titus; Poppels, Till; Levy, Roger P. Psychological Science, Vol. 31, Issue 2 https://doi.org/10.1177/0956797619890619	journal	January 2020
Multiple-Membership Survival Analysis and Its Applications in Organizational Behavior and Management Research Tierens, Hans; Dries, Nicky; Smet, Mike Organizational Research Methods, Vol. 24, Issue 2 https://doi.org/10.1177/1094428119877452	journal	September 2019
From Nuisance to Novel Research Questions: Using Multilevel Models to Predict Heterogeneous Variances Lester, Houston F.; Cullen-Lester, Kristin L.; Walters, Ryan W. Organizational Research Methods, Vol. 24, Issue 2 https://doi.org/10.1177/1094428119887434	journal	November 2019
Cardiac late events in German breast cancer patients: a validation study on the agreement between patient self-reports and information from physicians Merzenich, Hiltrud; Blettner, Maria; Niehoff, Dorothea BMC Cardiovascular Disorders, Vol. 18, Issue 1 https://doi.org/10.1186/s12872-018-0961-7	journal	November 2018
Orienting to polarized light at night—matching lunar skylight to performance in a nocturnal beetle Foster, James J.; Kirwan, John D.; el Jundi, Basil Journal of Experimental Biology https://doi.org/10.1242/jeb.188532	journal	January 2018
Atoh8 acts as a regulator of chondrocyte proliferation and differentiation in endochondral bones Schroeder, Nadine; Wuelling, Manuela; Hoffmann, Daniel PLOS ONE, Vol. 14, Issue 8 https://doi.org/10.1371/journal.pone.0218230	journal	August 2019
Temporal microstructure of dyadic social behavior during relationship formation in mice Lee, Won; Fu, Jiayi; Bouwman, Neal PLOS ONE, Vol. 14, Issue 12 https://doi.org/10.1371/journal.pone.0220596	journal	December 2019
Extending Bayesian back-calculation to estimate age and time specific HIV incidence. Brizzi, Francesco; Birrell, Paul; Plummer, Martyn T. Apollo - University of Cambridge Repository https://doi.org/10.17863/cam.37782	text	January 2019
Impairments in reinforcement learning do not explain enhanced habit formation in cocaine use disorder. Lim, Tsen Vei; Cardinal, Rudolf; Savulich, G. Apollo - University of Cambridge Repository https://doi.org/10.17863/cam.41843	text	January 2019
Comparison of serum and urinary biomarker panels with albumin/creatinine ratio in the prediction of renal function decline in type 1 diabetes Colombo, Marco; McGurnaghan, Stuart J.; Blackbourn, Luke A. K. Apollo - University of Cambridge Repository https://doi.org/10.17863/cam.53366	text	January 2020
Prediction of tool-wear in turning of medical grade cobalt chromium molybdenum alloy (ASTM F75) using non-parametric Bayesian models McParland, Damien; Baron, Szymon; O'Rourke, Sarah arXiv https://doi.org/10.48550/arxiv.1608.03091	preprint	January 2016
Robust Bayesian Model Selection for Variable Clustering with the Gaussian Graphical Model Andrade, Daniel; Takeda, Akiko; Fukumizu, Kenji arXiv https://doi.org/10.48550/arxiv.1806.05924	preprint	January 2018
Gender Bias in Nobel Prizes Lunnemann, Per; Jensen, Mogens H.; Jauffred, Liselotte arXiv https://doi.org/10.48550/arxiv.1810.07280	preprint	January 2018
Impact of using the ultra-high-energy cosmic ray arrival energies to constrain source associations Capel, Francesca; Mortlock, Daniel J. arXiv https://doi.org/10.48550/arxiv.1811.06464	text	January 2018
Probabilistic reanalysis of storm surge extremes in Europe Mir Calafat, Francisco; Marcos, Marta EGU General Assembly 2020 https://doi.org/10.5194/egusphere-egu2020-4888	posted_content	May 2020
A model for longitudinal data sets relating wind-damage probability to biotic and abiotic factors: a Bayesian approach Umeki, Kiyoshi; Abrams, Marc David; Toyama, Keisuke Forest Systems, Vol. 28, Issue 3 https://doi.org/10.5424/fs/2019283-15200	journal	November 2019
A New Model for Acquiescence at the Interface of Psychometrics and Cognitive Psychology Plieninger, Hansjörg; Heck, Daniel W. Figshare https://doi.org/10.6084/m9.figshare.6387803.v1	text	January 2018
Forecasting at Scale Taylor, Sean J.; Letham, Benjamin Peer J Preprints https://doi.org/10.7287/peerj.preprints.3190v1	posted_content	August 2017
Peer effects on control-averse behavior Rudorf, Sarah; Baumgartner, Thomas; Knoch, Daria Nature Publishing Group https://doi.org/10.7892/boris.128808	text	January 2019

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