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Robien’s and Modgraph’s Response on NMR Prediction Validation

June 6, 2007

Wolfgang Robien and Modgraph Consultants, Ltd. have responded to my latest comments and findings on the evaluation of our NMR predictions vs. the NMRShiftDB. 

Let me first begin by saying that over the last 24 hours, ACD/Labs was informed by Modgraph representation that my claims on this blog regarding CSEARCH and Modgraph’s NMRPredict were not clear. Since this time it has since been explained that while Wolfgang’s CSEARCH program is indeed the basis of NMRPredict, the commercial product includes different underlying databases and datafiles as well as additional enhancements, such as ‘auto-stereo recognition’, different utilization of solvent-dependent predictions and ‘BEST selection’, which MAY not be available in CSEARCH. 

It turns out that Robien’s average deviation of 2.22 ppm was based on his CSEARCH algorithm. So you may notice that in my previous entries, I have scratched out any inaccurate product mentions of NMRPredict. If you read Robien’s original posting you might be confused in the same way that I was since in Robien’s initial study (the study my response was based on) he referred to CSEARCH and NMRPredict as one and the same. As you can see in the comparison table, he is directly comparing CSEARCH/NMRPredict to NMRSHiftDB.

Additional comments from Robien:

“A few facts about CSEARCH/NMRPredict and NMRShiftDB(notice he is linking to the NMRPredict product description on the Modgraph website!!!)

“My cooperation partners, where either CSEARCH-spectra are available or CSEARCH-technology has been implemented, also within CSEARCH/NMRPredict other collection like SPECINFO has been implemented”

Keep in mind, this is my own personal blog and I have taken on a personal responsibility to inform the public on news and events in the world of NMR software. I see the above text as written by Robien and make my own conclusions. I took what Robien wrote and proceeded with my thoughts. It was not clear in Wolfgang’s original article that he was not using Modgraph’s NMRPredict. If he had mentioned it, then perhaps it would have been less confusing. But there are several mentions and links to NMRPredict and Modgraph throughout his web pages. 

ACD/Labs has also made the appropriate revisions to the official validation document that I posted on my blog. The revised version is here.

I want to stress that while this document mistakenly claimed a comparison with Modgraph’s NMRPredict, I believe that this document still represents a valid practice for the evaluation of prediction accuracy. Transparency within this validation study was the goal and I truly believe that this study represents a fair and unbiased way of properly performing a prediction accuracy validation on an independent data set.

With that in mind, Robien has since collaborated with Modgraph Consultants, LTD. and produced what they believe is a TRUE prediction accuracy evaluation of the NMRPredict product.

His findings reveal an overall average deviation of 1.40 ppm (compare to the ACD/CNMR Predictor deviation of 1.59 ppm).

So has Modgraph now definitely proven that indeed it is, “the most accurate carbon 13 NMR predictor in an independent evaluation?

The numbers suggest so, but please pay attention to the details within the study.

“For this evaluation the combined databases from CSEARCH and SPECINFO holding a total of 345,308 reference spectra were used. Based on this higher number of reference spectra a somewhat higher structural overlap between our databases and the NMRShiftDB-test data has been detected.”

In our document, we clearly state the structural overlap (57%) between our prediction database and the NMRShiftDB. This number is not provided by Modgraph. This number is extremely important to know, is it not? They mention “somewhat higher structural overlap” but what is it?

They base their final results on the following:

“In order to compensate for this, we have recalculated our overall average deviation of 1.40 ppm using the lower structural overlap as detected by ACD. The value of 1.40 ppm corresponds
to 92,927 known carbon environments and 121,209 unknown carbon environments – without this compensation our overall average deviation would be slightly better, but a comparison with ACD’s results would be impossible.”

I do not believe that this is a very scientific way to produce these results. It is certainly not a valid practice to compare directly with the results produced by ACD/CNMR Predictor. Which compounds (or chemical shifts) did they remove for their analysis?

For example, if they have 80% overlap between their database and the NMRShiftDB, which chemical shifts do they remove from their analysis to get to an overlap of 57%? (as they have to produce their final deviation of 1.40 ppm).

Why not state what the overlap with NMRShiftDB is, and then perform a validation on completely novel chemical shifts like we have done? Transparency and valid science was our priority during the creation of the validation document. As a result we stated the database overlap up front, and conducted two separate studies to inform the public of our performance under both circumstances.

So before we can make a final decision on performance, I think Modgraph needs to make very clear the following:

  1. What is the overlap between NMRShiftDB and Modgraph’s NMR prediction databases? Further, with several different database sources how much duplication of data exists across the databases and within the entire package?
  2. Once that overlap is removed from the dataset, what is the final deviation produced by NMRPredict?

I think this information needs to be made very clear from Modgraph before they can claim to be, “the most accurate carbon 13 NMR predictor in an independent evaluation?

We worked very hard to create a best practice for the validation of prediction accuracy on an independent data set. It is disappointing to see that the example was not followed in an attempt here by Modgraph to compare to our results.  Perhaps there is a better way. We are open for suggestions.

I hope that we are able to compare the performance in a truly fair and reliable way as to provide the public with the correct information!  

Finally, Jeff Seymour, Marketing Manager for Modgraph Consultants, Ltd. has issued a comment on my blog here:

http://acdlabs.typepad.com/my_weblog/2007/05/nmrshiftdb_acdl.html#comment-71790940

I want to highlight one comment specifically:

The average deviation in NMRPredict was 1.40 ppm compared to an average deviation of 1.59 ppm in ACD/CNMR Predictor version 10.5, already compensating for your somewhat smaller structural overlap.

Again, I ask…what is the structural overlap and once you compensate for that and remove it from the test set, what is your average deviation?

These numbers have NOT been published, and therefore this statement is dubious for the time being.

More information from Robien’s finding can be found via the link below:

http://nmrpredict.orc.univie.ac.at/csearchlite/Robien2Ryan_May31_2007.html

Modgraph’s announcement is here:

http://www.modgraph.co.uk/product_nmr_shiftdb.htm

EDIT: This conversation has continued in the following entries (in order):

http://acdlabs.typepad.com/my_weblog/2007/06/note-from-an-nm.html

http://acdlabs.typepad.com/my_weblog/2007/06/the_purgatory_d.html

http://acdlabs.typepad.com/my_weblog/2007/07/final-note-on-t.html

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