Markov chain Monte Carlo without likelihoods

Proceedings of the National Academy of Sciences of the United States of America
Paul MarjoramSimon Tavaré

Abstract

Many stochastic simulation approaches for generating observations from a posterior distribution depend on knowing a likelihood function. However, for many complex probability models, such likelihoods are either impossible or computationally prohibitive to obtain. Here we present a Markov chain Monte Carlo method for generating observations from a posterior distribution without the use of likelihoods. It can also be used in frequentist applications, in particular for maximum-likelihood estimation. The approach is illustrated by an example of ancestral inference in population genetics. A number of open problems are highlighted in the discussion.

References

Jan 1, 1992·Journal of Molecular Evolution·J L ThorneJ Felsenstein
Oct 1, 1991·Proceedings of the National Academy of Sciences of the United States of America·R H WardS Pääbo
Feb 1, 1997·Molecular Biology and Evolution·Y X Fu, W H Li
Dec 22, 1999·Molecular Biology and Evolution·J K PritchardM W Feldman

Citations

Apr 26, 2007·Bulletin of Mathematical Biology·Alex CookGavin Gibson
Dec 25, 2010·Bulletin of Mathematical Biology·Raazesh SainudiinPeter Donnelly
Jan 8, 2013·Bulletin of Mathematical Biology·Brad WeirYvette H Spitz
May 7, 2013·Journal of Theoretical Biology·Anne Kandler, Kevin N Laland
Apr 21, 2011·Environmental Science & Technology·Jörg RieckermannChristoph Ort
Jun 14, 2013·Heredity·Paul MarjoramS V Nuzhdin
Aug 28, 2012·Nature Genetics·James X SunKari Stefansson
May 8, 2004·Nature Reviews. Genetics·Mark A Beaumont, Bruce Rannala
Aug 23, 2006·Nature Reviews. Genetics·Laurent Excoffier, Gerald Heckel
Sep 20, 2006·Nature Reviews. Genetics·Paul Marjoram, Simon Tavaré
Oct 3, 2009·Molecular BioSystems·Maria SecrierMichael P H Stumpf
Jun 16, 2009·Proceedings of the National Academy of Sciences of the United States of America·Oliver RatmannSylvia Richardson
Jan 9, 2013·Proceedings of the National Academy of Sciences of the United States of America·Kerrie L MengersenChristian P Robert
Jan 8, 2011·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Paul A Jenkins, Robert C Griffiths
Feb 7, 2012·American Journal of Epidemiology·Stephen R ColeDavid B Richardson
Mar 17, 2009·Bioinformatics·Xavier DidelotDaniel Falush
Aug 15, 2009·Bioinformatics·Joao LopesMark A Beaumont
Feb 2, 2010·Molecular Biology and Evolution·Daniel Wegmann, Laurent Excoffier
Dec 12, 2012·Interface Focus·Chris P BarnesMichael P H Stumpf
Feb 11, 2009·Journal of the Royal Society, Interface·Tina ToniMichael P H Stumpf
Apr 20, 2012·Journal of the Royal Society, Interface·Francisco J Pérez-RecheChristopher A Gilligan
Oct 5, 2012·Journal of the Royal Society, Interface·J Conrad StackBryan Grenfell
Dec 7, 2013·Journal of the Royal Society, Interface·Alejandro F Villaverde, Julio R Banga
Dec 28, 2011·Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences·Michael W Nachman, Bret A Payseur
Mar 6, 2010·BMC Bioinformatics·Daniel WegmannLaurent Excoffier
Oct 27, 2007·BMC Bioinformatics·Dario GasbarraElja Arjas
Nov 16, 2010·Human Genomics·Duncan C ThomasCornelia M Ulrich
Jul 5, 2012·PLoS Computational Biology·R Zachariah AandahlMark M Tanaka
Jan 24, 2013·PLoS Computational Biology·Mikael SunnåkerChristophe Dessimoz
Feb 6, 2013·PLoS Computational Biology·Juliane LiepeMichael P H Stumpf

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Hereditary Sensory Autonomic Neuropathy

Hereditary Sensory Autonomic Neuropathies are a group of inherited neurodegenerative disorders characterized clinically by loss of sensation and autonomic dysfunction. Here is the latest research on these neuropathies.

Glut1 Deficiency

Glut1 deficiency, an autosomal dominant, genetic metabolic disorder associated with a deficiency of GLUT1, the protein that transports glucose across the blood brain barrier, is characterized by mental and motor developmental delays and infantile seizures. Follow the latest research on Glut1 deficiency with this feed.

Regulation of Vocal-Motor Plasticity

Dopaminergic projections to the basal ganglia and nucleus accumbens shape the learning and plasticity of motivated behaviors across species including the regulation of vocal-motor plasticity and performance in songbirds. Discover the latest research on the regulation of vocal-motor plasticity here.

Neural Activity: Imaging

Imaging of neural activity in vivo has developed rapidly recently with the advancement of fluorescence microscopy, including new applications using miniaturized microscopes (miniscopes). This feed follows the progress in this growing field.

Nodding Syndrome

Nodding Syndrome is a neurological and epileptiform disorder characterized by psychomotor, mental, and growth retardation. Discover the latest research on Nodding Syndrome here.

LRRK2 & Microtubules

Mutations in the LRRK2 gene are risk-factors for developing Parkinson’s disease (PD). LRRK2 mutations in PD have been shown to enhance its association with microtubules. Here is the latest research.