include weights in tICA

[euhruska]

Is it possible to add including weights when calculating tICA from multiple trajectories? Each trajectory would have different (non-integer) weights.

[gph82]

Hi, can you be a bit more specific as to what will happen to the transformed trajectories once you computed your weighted TICA transformation? Normal discretization plus MSM, like in the example notebooks?

[euhruska]

no MSM, at least, I don't plan to. I want to do then a reweighting step similar to DM-d-MD. That's why the weights are quite important. For that, I only need the TICA coordinates of the points along the trajectories.

[gph82]

I am not familiar with the new running_covar class, perhaps one could provide it with an array of trajectory weights at initialization and then set return_trajindex = True for this iterator
https://github.com/markovmodel/PyEMMA/blob/devel/pyemma/coordinates/transform/tica.py#L264
and parse that trajindex to self._covar.add here:
https://github.com/markovmodel/PyEMMA/blob/devel/pyemma/coordinates/transform/tica.py#L268

but I am not sure if the running_moments algorithm assumes equal weights. What do you think, @franknoe

[franknoe]

Don't worry, I'll do it. I just told Eugen to open an issue so that I
don't forget.

Am 30/03/16 um 18:07 schrieb Guillermo Pérez-Hernández:

I am not familiar with the new running_covar class, perhaps one could
provide it with an array of trajectory weights at initialization and
then set |return_trajindex = True| for this iterator
https://github.com/markovmodel/PyEMMA/blob/devel/pyemma/coordinates/transform/tica.py#L264
and parse that trajindex to |self._covar.add| here:
https://github.com/markovmodel/PyEMMA/blob/devel/pyemma/coordinates/transform/tica.py#L268

but I am not sure if the running_moments algorithm assumes equal
weights. What do you think, @franknoe https://github.com/franknoe

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#749 (comment)

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Prof. Dr. Frank Noe
Head of Computational Molecular Biology group
Freie Universitaet Berlin

Phone: (+49) (0)30 838 75354
Web: research.franknoe.de

Mail: Arnimallee 6, 14195 Berlin, Germany

[marscher]

Isn't that just a duplicate of #570?

[franknoe]

It is indeed!
Feliks is currently working on that.

Am 17/05/16 um 20:18 schrieb Martin K. Scherer:

Isn't that just a duplicate of #570
#570?

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#749 (comment)

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Prof. Dr. Frank Noe
Head of Computational Molecular Biology group
Freie Universitaet Berlin

Phone: (+49) (0)30 838 75354
Web: research.franknoe.de

Mail: Arnimallee 6, 14195 Berlin, Germany

[marscher]

Ok. I'll close the older issue then

[marscher]

I think we have this now