I’ve written a few posts now about using parallel tempering to sample from complicated multi-modal target distributions but there are also other benefits and uses to this algorithm. There is a nice post on Darren Wilkinson’s blog about using tempered posteriors for marginal likelihood calculations. There is also another area where parallel tempering finds application, […]The post Stochastic Optimization in R by Parallel Tempering appeared first on Lindons Log.... Read more »
Li Yaohang, Protopopescu Vladimir A., Arnold Nikita, Zhang Xinyu, & Gorin Andrey. (2009) Hybrid parallel tempering and simulated annealing method. Applied Mathematics and Computation, 212(1), 216-228. DOI: 10.1016/j.amc.2009.02.023
Bone cracks can be detected by utilizing the damaged matrix itself as both the trigger and the fuel. A crack in a material with a high mineral content such as bone generates ion gradients, which can be utilized for active targeting and treatment. This approach to targeting a biological structure augments current methods, which are focused on biomacromolecular interactions involving proteins and nucleic acids.... Read more »
Yadav V, Freedman JD, Grinstaff M, & Sen A. (2013) Bone-Crack Detection, Targeting, and Repair Using Ion Gradients. Angewandte Chemie (International ed. in English). PMID: 24039057
Have you always wanted a 3-D printer but never really had a justification for the investment? Well, a study done by Michigan technological University has your back. It shows that in many cases 3-D printing products are more environmentally friendly than mass production.... Read more »
Christian Baechler, Matthew DeVuono, Joshua M. Pearce. (2013) Distributed recycling of waste polymer into RepRap feedstock. Rapid Prototyping Journal. DOI: 10.1108/13552541311302978
Yesterday, I shared a video of John Maynard Smith introducing evolutionary game theory (EGT) to the London Mathematical Society. I suggested that at its foundation, EGT was just like classical game theory, and based on equilibrium analysis — the evolutionary stable strategy (Maynard Smith & Price, 1973). Given a utility function that gives the expected […]... Read more »
Conitzer, V. (2013) The exact computational complexity of evolutionarily stable strategies. The 9th Conference on Web and Internet Economics (WINE). info:/
This honeybee swarm has precious little time to make a democratic decision as to where they will move to. A decision deadlock could have fatal consequences. Image by Nino Barbieri at Wikimedia Commons.In case you've been living in a cave lately, the U.S. Government has been shut down since October 1st. Not because of a terrorist attack or a bank system meltdown or a natural disaster, but because Congress cannot agree on a spending bill to determine our government's funding plan for the next year. The government shutdown has its consequences (such as closed national parks, postponed federal research funding, the halting of the CDC's flu vaccine program, and unpaid federal employees), but these will seem like a slap on the wrist if Congress can't agree to raise the debt ceiling by October 17. If we are still in a government deadlock at that point, we will default on our national loans and suffer disastrous consequences (such as the devaluation of the dollar, social security payments not being made, spiking interest rates, and devaluation and forced selling off of bonds). Congress is up against a deadline to make a group decision, and the consequences of not making one in time are much higher than the consequences of making an inperfect one. It's hard to come to a consensus when so many individuals in the group have a strong opinion one way or another, but the fact of the matter is: honeybees can do it. So why can't we? This week at Accumulating Glitches I tell the story of how honeybees democratically decide on what new home to move to, all while avoiding a deadlock at indecision. Check it out here.And to learn more, check these out: Seeley, T.D., Visscher, P.K., Schlegel, T., Hogan, P.M., Franks, N.R., & Marshall, J.A.R. (2012). Stop signals provide cross inhibition in collective decision-making by honeybee swarms Science, 335, 108-111 DOI: 10.1126/science.1210361Seeley, T.D. Honeybee Democracy, Princeton University Press (2010). And learn more about group decision-making in animals at Can a Horde of Idiots Be a Genius? and Why This Horde of Idiots Is No Genius ... Read more »
Seeley, T.D., Visscher, P.K., Schlegel, T., Hogan, P.M., Franks, N.R., & Marshall, J.A.R. (2012) Stop signals provide cross inhibition in collective decision-making by honeybee swarms. Science, 108-111. DOI: 10.1126/science.1210361
Researchers have presented the first public version (v0.2) of the open-source and community-developed Python package, Astropy, that is able to provide core astronomy-related functionality to the community.
Astronomy & Astrophysics
Python is a portable, interpreted, object-oriented programming language developed and freely distributed by its developer. Python runs on many platforms, including UNIX, Windows, OS/2 and Macintosh and is used for writing TCP/IP applications.
Python is one of the largest growing languages in the astronomy community in the last decade.
The Astropy project was started in 2011 with the desire to bring the astronomy related developers together to make progress in the development of Python tools for astronomers.
Researchers have presented the first public release of the Astropy package (v0.2) i.e., a Python package for astronomers. Researchers have described the main functionality of the package in the present research.
This main functionality includes “the support for domain-specific file formats such as flexible image transport system (FITS) files, Virtual Observatory (VO) tables, and common ASCII table formats, unit and physical quantity conversions, physical constants specific to astronomy, celestial coordinate and time transformations, world coordinate system (WCS) support, generalized containers for representing gridded as well as tabular data, and a framework for cosmological transformations and conversions.”
To study the further details of presentation or to check the package, you can see the reference.
Astropy - A community Python Library for Astronomy (http://docs.astropy.org/en/stable/)
The Astropy Collaboration, & Thomas P. Robitaille et al. (2013). Astropy: A community Python package for astronomy Astronomy & Astrophysics DOI: 10.1051/0004-6361/201322068... Read more »
Biologists of the University of Zurich have developed a method to visualize the activity of genes in single cells. The method is so efficient that, for the first time, a thousand genes can be studied in parallel in ten thousand single human cells. Applications lie in fields of basic research and medical diagnostics. The new method shows that the activity of genes, and the spatial organization of the resulting transcript molecules, strongly vary between single cells.... Read more »
Nico Battich, Thomas Stoeger, & Lucas Pelkmans. (2013) Image-based transcriptomics in thousands of single human cells at single-molecule resolution. Nature Methods. DOI: 10.1038/nmeth.2657
My office computer recently got a really nice upgrade and now I have 8 cores on my desktop to play with. I also at the same time received some code for a Gibbs sampler written in R from my adviser. I wanted to try a metropolis-coupled markov chain monte carlo, , algorithm on it to […]The post Parallel Tempering in R with Rmpi appeared first on Lindons Log.... Read more »
Earl David J., & Deem Michael W. (2005) Parallel tempering: Theory, applications, and new perspectives. Physical Chemistry Chemical Physics, 7(23), 3910. DOI: 10.1039/b509983h
Time-to-publication at the world’s biggest scientific journal has grown dramatically, but the nail in the coffin was its poor production policies. When PLOS ONE was announced in 2006, its charter immediately resonated with me. This would be the first journal where only scientific accuracy mattered. Judgments of “impact” and “interest” would be left to posterity, […]... Read more »
Nunez-Iglesias J, Liu CC, Morgan TE, Finch CE, & Zhou XJ. (2010) Joint genome-wide profiling of miRNA and mRNA expression in Alzheimer's disease cortex reveals altered miRNA regulation. PloS one, 5(2). PMID: 20126538
Kravitz DJ, & Baker CI. (2011) Toward a new model of scientific publishing: discussion and a proposal. Frontiers in computational neuroscience, 55. PMID: 22164143
Juan Nunez-Iglesias, Ryan Kennedy, Toufiq Parag, Jianbo Shi, & Dmitri B. Chklovskii. (2013) Machine learning of hierarchical clustering to segment 2D and 3D images. arXiv. arXiv: 1303.6163v3
Nunez-Iglesias J, Kennedy R, Parag T, Shi J, & Chklovskii DB. (2013) Machine Learning of Hierarchical Clustering to Segment 2D and 3D Images. PloS one, 8(8). PMID: 23977123
New research led by an electrical engineer at the University of California, San Diego is aimed at improving lithium-ion batteries through possible new electrode architectures with precise nano-scale designs.... Read more »
Liu Y, Liu XH, Nguyen BM, Yoo J, Sullivan J, Picraux ST, Huang JY, & Dayeh SA. (2013) Tailoring Lithiation Behavior by Interface and Bandgap Engineering at the Nanoscale. Nano Letters. PMID: 24000810
UCLA chemical engineering researchers have created a new synthetic metabolic pathway for breaking down glucose that could lead to a 50 percent increase in the production of biofuels.... Read more »
Igor W. Bogorad, Tzu-Shyang Lin, James C. Liao. (2013) Synthetic non-oxidative glycolysis enables complete carbon conservation. Nature. DOI: 10.1038/nature12575
“Gentlemen, we can rebuild him. We have the technology. We have the capability to make the world’s first bionic man. Steve Austin will be that man. Better than he was before. Better…stronger…faster.”
Readers of a certain age will tingle with recognition at those words, intoned over the intro to ’70s TV series “The Six Million Dollar Man“, promising the bodily reconstruction of a seriously injured astronaut. Back then it was distant science fiction, but fast-forward 30 years to 2003, and a very shiny new PLOS Biology published a paper in its second ever issue that did indeed “have the technology”...... Read more »
Carmena JM, Lebedev MA, Crist RE, O'Doherty JE, Santucci DM, Dimitrov DF, Patil PG, Henriquez CS, & Nicolelis MA. (2003) Learning to control a brain-machine interface for reaching and grasping by primates. PLoS biology, 1(2). PMID: 14624244
Computer scientists that think of nature as literally computing, often take the stance that biological organisms are nothing more than protein interaction networks. For example, this is the stance that Leslie Valiant (2009) takes when defining ecorithms: biology is just a specialization of computer science focused on evolvable circuits. User @exploderator summarized the realist computational […]... Read more »
Two weeks ago, I lectured on how we can minimize and learn deterministic finite state automata. Although it might not be obvious, these lectures are actually pretty closely related since minimization and learning often go hand-in-hand. During both lectures I hinted that the results won’t hold for non-deterministic finite state automata (NFA), and challenged the […]... Read more »
A University of Virginia engineering professor has proposed a novel approach for keeping waste carbon dioxide out of the atmosphere.... Read more »
Tao Z., Clarens A. (2013) Estimating the Carbon Sequestration Capacity of Shale Formations Using Methane Production Rates. Environmental Science and Technology. PMID: 23988277
Before her mother convinced her to be a doctor, my mother was a ballerina. As a result, whenever I tried to blame some external factor for my failures, I was met with my mother’s favorite aphorism: a bad dancer’s shoes are always too tight. “Ahh, another idiosyncratic story about the human side of research,” you […]... Read more »
Livnat A, & Pippenger N. (2008) Systematic mistakes are likely in bounded optimal decision-making systems. Journal of Theoretical Biology, 250(3), 410-23. PMID: 18022645
According to a study by Georgia Tech researchers, the advantages of electric versus diesel depend largely on how the trucks will be used—the frequency of stops and average speeds—and the source of electricity for charging batteries. In city driving with frequent stops, the electric trucks clearly outperform diesel vehicles, while diesel vehicles show better efficiency in suburban routes.... Read more »
Dong-Yeon Lee, Valerie M. Thomas and Marilyn A. Brown. (2013) “Electric Urban Delivery Trucks: Energy Use, Greenhouse Gas Emissions, and Cost Effectiveness. Environmental Science , 47(14), 8022-8030. DOI: 10.1021/es400179w
According to British historian Arnold Toynbee, “History is just one damned thing after another.” Or is it? That is the question Peter Turchin of the University of Connecticut in Storrs tries to answer in a new study just published in the Proceedings of the National Academy of Sciences. He and his colleagues show history may be deterministic, at least to a certain extent. Their computer simulations show that warfare may have been the main driver behind the formation of empires, bureaucracies and religions.... Read more »
Peter Turchin et al. (2013) War, space, and the evolution of Old World complex societies. Proceedings of the National Academy of Sciences of the United States of America PNAS, Proceedings of the National Academy of Sciences. DOI: 10.1073/pnas.1308825110
Many graduate students, and even professors, have a strong aversion to teaching. This tends to produce awful, one-sided classes that students attend just to transcribe the instructor’s lecture notes. The trend is so bad that in some cases instructors take pride in their bad teaching, and at some institutions — or so I hear around […]... Read more »
Angluin, D. (1987) Learning regular sets from queries and counterexamples. Information and Computation,, 87-106. DOI: 10.1016/0890-5401(87)90052-6
About 90% of all electricity is generated using steam as the working fluid, nearly all by steam turbines. In electric generation, steam is typically condensed at the end of its expansion cycle, and returned to the boiler for re-use. A technology that improves steam condenser efficiency could have a large impact on global electricity generation. Now a team of scientists from MIT has found a way to do this.... Read more »
Adam T. Paxson, Jose L. Yagüe, Karen K. Gleason, Kripa K. Varanasi. (2013) Stable Dropwise Condensation for Enhancing Heat Transfer via the Initiated Chemical Vapor Deposition (iCVD) of Grafted Polymer Films. Advanced Materials. DOI: 10.1002/adma.201303065
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