[FRIAM] Weighted Ensemble

Mon Aug 30 15:22:26 EDT 2021

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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