choderalab / bayesian-itc

Python tools for the analysis and modeling of isothermal titration calorimetry (ITC) experiments.
GNU General Public License v3.0
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Baseline fitting algorithm #17

Open bas-rustenburg opened 9 years ago

bas-rustenburg commented 9 years ago

The currently implemented algorithm in python/bayesianitc/experiments does not perform well.

@pgrinaway experimented once with gaussian processes.

That said, we can also use origin files now to override the integrated heats. NITPIC also produces a .dat file with origin style formatting that ITC.py can read with the -q command line option.

bas-rustenburg commented 9 years ago

@pgrinaway just mentioned possibly using gptools.

bas-rustenburg commented 9 years ago

I've implemented a gaussian process fit in #22. For now, we still calculate the integrated heats, but we should add the baseline parameters to the model at a later date.

bas-rustenburg commented 9 years ago

Slight clarification: The choices for the gaussian process fitting parameters are arbitrary numbers that worked when I experimented with sklearn.

Here is where they are declared.

jchodera commented 9 years ago

I bet these can be selected by either cross-validation or (my preference) inference (using some hyperparameters) with some calibration datasets (e.g. long experiments without injections).