[FRIAM] Weighted Ensemble

Mon Aug 30 15:52:34 EDT 2021

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 <rec at elf.org> 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 <marcus at snoutfarm.com>
> 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 <friam-bounces at redfish.com> On Behalf Of u?l? ?>$
>> Sent: Monday, August 30, 2021 11:27 AM
>> To: friam at redfish.com
>> 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[\"]* <
>> rec at elf.org>" *))) 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 ☤>$ <gepropella at gmail.com> 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
>>
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>
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