There is also an implementation of weighted ensembles in julia, last updated 8 days ago.
https://github.com/gideonsimpson/WeightedEnsemble.jl juliahub.com sells julia instances in the cloud, the first few are free. -- rec -- On Mon, Aug 30, 2021 at 3:22 PM Roger Critchlow <[email protected]> wrote: > Not a bad rant, sounds like Nick´s emergent book club, but that is not the > rant I was looking for. > > Yah, found the references the hard way. > > The paper from LANL was > https://journals.aps.org/prb/abstract/10.1103/PhysRevB.57.R13985, > pretty bad job on producing the date and author name. > > Parallel replica method for dynamics of infrequent eventsArthur F. VoterPhys. > Rev. B 57, R13985(R) – Published 1 June 1998 > > The Pande lab paper was > https://journals.aps.org/prl/abstract/10.1103/PhysRevLett.86.4983 > > Mathematical Analysis of Coupled Parallel SimulationsMichael R. Shirts > and Vijay S. PandePhys. Rev. Lett. 86, 4983 – Published 28 May 2001 > i found the first from the second, found the second as #181/260 in the > Pubmed listing for "pande vs" which the Pande lab uses as its list of > publications. > > I originally picked up on the topic in > https://science.sciencemag.org/content/290/5498/1903 > Screen Savers of the World Unite! > > 1. Michael Shirts > <https://science.sciencemag.org/content/290/5498/1903#aff-1>, > 2. Vijay S. Pande* > <https://science.sciencemag.org/content/290/5498/1903#aff-1> > > See all authors and affiliations > Science 08 Dec 2000: > Vol. 290, Issue 5498, pp. 1903-1904 > DOI: 10.1126/science.290.5498.1903 > So the original rant might have been on a BiosGroup mailing list or just > in my head. > -- rec -- > > On Mon, Aug 30, 2021 at 2:33 PM Marcus Daniels <[email protected]> > wrote: > >> This week's Science has an article on predicting RNA structure using deep >> learning. The other approach you mention sounds like Rosetta. >> >> -----Original Message----- >> From: Friam <[email protected]> On Behalf Of u?l? ?>$ >> Sent: Monday, August 30, 2021 11:27 AM >> To: [email protected] >> Subject: Re: [FRIAM] Weighted Ensemble >> >> The below is the only thing my search turns up (via $ grep -i folding >> $(grep -li protein $(grep -l "From: [\"]*Roger Critchlow[\"]* < >> [email protected]>" *))) I found nothing if I include "parallel" in the and. >> If you have other keywords, maybe it'll be more apparent. (Header still >> includes Google. So it's not clear to me when you started using GMail.) >> >> >> On 9/14/09 7:48 PM, Roger Critchlow wrote: >> > As I read it, the issue isn't whether structures and/or configurations >> > are/aren't important, the question is whether they operate according >> > to emergent or resultant rule sets. >> > >> > The Emergentists were betting heavily on the emergent rule set. They >> > believed that the variety of chemistry couldn't possibly be the result >> > of protons and electrons operating according to physics as they knew >> > it. They were right, it wasn't physics as they knew it, but the >> > answer turned out to be the result of configurational physics rather >> > than emergent principles of chemistry. They also bet that the variety >> > of biology couldn't be the result of chemical molecules operating >> > according to the chemistry they knew. And they were right again, it >> > wasn't chemistry as they knew it, but the answer turned out to be the >> > result of configurational chemistry rather than emergent priniciples >> > of biology. >> > >> > Chemistry and biology turn out to be ever more complicated >> > configurations of protons and electrons, with some neutron ballast, >> > operating according to the principles of quantum mechanics and >> > statistical mechanics. It's all physics, same particles, same forces, >> > same laws, no emergent forces. There are configuration forces, but >> > they're not emergent forces, they're subtle results of electrons >> > packing themselves into quantized energy levels in increasingly >> > complicated configurations of nuclei. >> > >> > The structure of DNA and the elaboration of molecular biology was the >> > last straw because it provided a purely physical mechanism for >> > inheritance. >> > >> > But you're right to see it as a bit of a conundrum. The Emergentists, >> > as McLaughlin summarizes them, were substantially correct: >> > configurations of atoms in molecules are the key to understanding >> > chemistry, there are all sorts of chemically distinctive things that >> > happen because of those configurations, none of those chemically >> > distinctive things are obvious when you play around with protons and >> > electrons in the physics lab. But it all turned out to be part of the >> > resultant of quantum mechanics, not emergent in the sense the >> > Emergentists had painted themselves into, so they were wrong in the >> > one sense they really cared about. >> >> >> >> >> On 8/30/21 10:43 AM, Roger Critchlow wrote: >> > This sounds like an algorithm for parallel protein folding that I >> > ranted about a long time ago. Start with some collection of >> > conformations; perform many different molecular dynamics simulations >> > from your starting points in parallel; continue with the most >> > promising subset. As molecular dynamics on proteins tends to find >> > lots of deadends, you can get a lot of improvement by tabu'ing the >> > known deadends and extending into conformations which don't double >> > back into visited regions. Seems I remember it went back to some >> monte-carlo work at LANL in the 1950's, Goodfellow? >> > >> > It also sounds a lot like Monte Carlo Tree search as used, for >> > instance, in AlphaGo. >> > >> > It boils down to how well you can distinguish promising and >> > unpromising branches. >> > >> > Whatever, it was in Friam before gmail, so I can't search for it. >> > There doesn't appear to be any search in the Friam archives, and the >> > years before >> > 2017 at https://redfish.com/pipermail/friam_redfish.com/ are all 404 >> anyway. >> > >> > -- rec -- >> > >> > On Mon, Aug 30, 2021 at 12:39 PM uǝlƃ ☤>$ <[email protected]> wrote: >> > >> >> In my ignorance, I've thought of weighted ensemble (WE) as a specific >> >> kind of novelty search. E.g. weighting toward trajectories that >> >> exhibit anomalies. Is that what you mean by it? >> >> >> >> Also, for each of the 5 you're interested in, do you have convenient >> >> example cites for each/any of them? In particular, (2) and (3)? Or >> >> are these just ideas of places where you think WE should apply? >> >> >> >> For my part, no. I haven't used WE in particular. I have a friend >> >> who's worked on identifying mechanical anomalies from audio >> >> (recordings of machines as they hum). He may have used it. I'll ask. >> >> >> >> On 8/29/21 1:07 PM, Jon Zingale wrote: >> >>> I am presently working on learning weighted ensemble < >> >> https://arxiv.org/pdf/1906.00856.pdf> sampling techniques and was >> >> curious if any here have worked with them before. The technique seems >> >> promising and has enjoyed quite a bit of success (even above MCMC < >> >> https://en.wikipedia.org/wiki/Markov_chain_Monte_Carlo>) in circles >> >> concerned with reaction rates for rare events. >> >>> >> >>> Some points of interest for me include: >> >>> >> >>> 1. A better sampling of fringe-outlier works/art from streaming >> >> services. >> >>> 2. An alternative (bin-based sampling) to globally defined "fitness" >> >> measures in evolutionary modeling. >> >>> 3. An application of diffusion-limited aggregation to general >> >>> search >> >> (especially in the face of limited resources) >> >>> 4. An application of linear logic to optimization problems in >> >> conformation prediction < >> >> https://en.wikipedia.org/wiki/Protein_structure_prediction>. >> >>> 5. Investigation of dynamical properties, such as distribution of >> >> trajectories with "high winding number", on strange attractors. >> >>> >> >>> >> >>> While I am just beginning to grok the technique, I thought it might >> >>> be >> >> fruitful to ask here. >> >> >> -- >> ☤>$ uǝlƃ >> >> - .... . -..-. . -. -.. -..-. .. ... -..-. .... . .-. . >> FRIAM Applied Complexity Group listserv >> Zoom Fridays 9:30a-12p Mtn GMT-6 bit.ly/virtualfriam un/subscribe >> http://redfish.com/mailman/listinfo/friam_redfish.com >> FRIAM-COMIC http://friam-comic.blogspot.com/ >> archives: http://friam.471366.n2.nabble.com/ >> - .... . -..-. . -. -.. -..-. .. ... -..-. .... . .-. . >> FRIAM Applied Complexity Group listserv >> Zoom Fridays 9:30a-12p Mtn GMT-6 bit.ly/virtualfriam >> un/subscribe http://redfish.com/mailman/listinfo/friam_redfish.com >> FRIAM-COMIC http://friam-comic.blogspot.com/ >> archives: http://friam.471366.n2.nabble.com/ >> >
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