Re: [Cuitools-users] --mesh option

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Hi Ted,

This sounds good. I will add it!

Thanks,

Bridget

On Thu, 24 Jul 2008, Ted Pedersen wrote:

> Hi Bridget,
>
> In your INSTALL document, I think we probably want to clarify what
> people should be downloading by giving not only what they see on the
> link (which you have below) but also the names of the files they get.
> Also, I think what they download from the full test collection are the
> first and second files there...?
>
> I see that you say in the INSTALL document we should use the PMID
> version, and that seems fine to me...I did not use the PMID version
> when I did my install so I'm going back to use PMID....
>
> ========================
> The first in the ``Basic Test Collection'': 1. Basic Reviewed Set
>
> The second and third in the ``Full Test Collection'': 2. Common Files
> 3. Full Reviewed Result Set
>
> Unpack the files in a directory called NLM-WSD (for example - you can
> call it anything you would like). You should end up with three
> directories in the NLM-WSD directory: 1. Basic_Reviewed_Results 2.
> common 3. Reviewed_Results
> =========================
>
> We may also want caution the user that the file names for the PMID and
> non-PMID versions are the same, and give them some idea of how to tell
> them apart...and we should probably still have a check somewhere that
> automatically verifies that we have the PMID format, not only in the
> event that people download the wrong version, but that they might try
> to use completely wrong sorts of data....
>
> Thanks!
> Ted
>
> On Thu, Jul 24, 2008 at 10:49 AM, Ted Pedersen <tpederse@d.umn.edu> wrote:
> > Hi Bridget,
> >
> > One small question below...
> >
> > On Wed, Jul 23, 2008 at 4:00 PM, Bridget Thomson McInnes
> > <bth...@cs...> wrote:
> >> Hi Ted,
> >>
> >> You are using the wrong version of the NLM-WSD dataset. There are two
> >> version, one in which the identifiers are PMIDs and the other which are UIs.
> >> Unfortuently, the UIs one is the first one.
> >>
> >> If you go to the NLM-WSD website: http://wsd.nlm.nih.gov/
> >>
> >> and log in, scroll down to the first white box. You will see:
> >>
> >>  Switch to PMID identified version of the WSD Test Collection
> >>
> >>
> >> It originally didn't matter which version that you used but now when using
> >> the --mesh option or running the make-MMTxNLM-data.sh Demo - the PMID
> >> version is required.
> >
> > I think I'm running the make-MMTxNLM-data.sh script on the same data I'm using
> > for everything else (which isn't probably the PMID data....) Is there something
> > I should see in the output that would let me know that it wasn't the PMID data?
> >
> > I can't remember if I asked this before, but I'm wondering if we should simply
> > require the PMID data, to avoid having the user get two different
> > forms of the same
> > data (and potentially use them in the wrong places...) It sounds like
> > some things
> > will work with both forms of the data, but a few things will not (and require
> > PMID), so that sort of suggests that PMID is the more "generic" form of the
> > data....is there any downside to using PMID rather than the other form?
> >
> > Related to this, are there any other possible enhancements in the
> > future (that we've
> > already discussed) that would require PMID?
> >
> > What do you think?
> >
> > Thanks,
> > Ted
> >
> >>
> >> I will think about how to go about adding a check for that. I have done it
> >> myself to many times as well. And state it clearer in the INSTALL
> >> documentation.
> >>
> >> Sorry about that!
> >>
> >> Thanks,
> >>
> >> Bridget
> >>
> >> On Wed, 23 Jul 2008, Ted Pedersen wrote:
> >>
> >>> Hi Bridget,
> >>>
> >>> I'm using whichever one is used by the McInnes07 demo, since I'm just
> >>> copying McInnes07.mm and using that as TDP.mm.
> >>>
> >>> Here's the first few lines of adjustment.mm, hopefully that will make
> >>> it clear what I'm using - I *think* this is the PMID version since it
> >>> has that number in it (which I think is the PMID)?
> >>>
> >>> <corpus lang='en'>
> >>>  <lexelt item="adjustment" senses="M1,M2,M3,None">
> >>>   <instance id="98076825" alias="adjustment">
> >>>     <answer instance="98076825.ab.7" senseid="M2"/>
> >>>     <context line="Influence of physiological factors on the
> >>> age-related increase in blood pressure in healthy men. The independent
> >>> a
> >>> nd collective influences of several physiological factors on the
> >>> age-related increase in blood pressure in healthy men were examined. T
> >>> wenty-seven younger and 25 older, mostly normotensive, healthy men
> >>> were studied. Blood pressure, body fat, body fat distribution, maxim
> >>> al oxygen consumption (VO2max), plasma norepinephrine, dietary Na, and
> >>> erythrocyte Na-K pump activity were measured. Older men showed 5
> >>> 7% higher percent body fat, 40% higher plasma norepinephrine
> >>> concentration, 14% greater mean arterial blood pressure (MAP), and 5%
> >>> high
> >>> er plasma K concentration than younger men (all p < 0.01). Older men
> >>> showed a 38% (p < 0.01) lower VO2max, 19% (p < 0.05) lower energy
> >>> intake, 18% (p < 0.05) lower Na-K pump rate constant, and a 17% (p <
> >>> 0.05) lower Na-K pump rate. Group means for MAP were adjusted for
> >>> combinations of plasma norepinephrine, waist:thigh ratio, VO2max, and
> >>> the Na-K pump rate constant, to determine if any one variable or
> >>> combination could account for the age related increase in MAP.
> >>> Statistical adjustment for plasma norepinephrine, waist:thigh ratio,
> >>> and
> >>> Na-K pump rate constant eliminated the significant difference between
> >>> MAPs for the two groups. Thus, alterations in sympathetic nervou
> >>> s system activity, body fat distribution, and the membrane Na-K pump
> >>> activity independently contribute to the age-related increase in M
> >>> AP in healthy men. "/>
> >>>       <sentence tw="" id="98076825.ti.1" line="Influence of
> >>> physiological factors on the age-related increase in blood pressure in
> >>> he
> >>> althy men.">
> >>>
> >>> Does that look like the right format?
> >>>
> >>> Thanks!
> >>> Ted
> >>>
> >>> On Wed, Jul 23, 2008 at 3:30 PM, Bridget Thomson McInnes
> >>> <bth...@cs...> wrote:
> >>>>
> >>>> Hi Ted,
> >>>>
> >>>> What version of the NLM-WSD dataset are you using? The --mesh option
> >>>> requires that the PMID version be used.
> >>>>
> >>>> Thanks!
> >>>>
> >>>> Bridget
> >>>>
> >>>> On Wed, 23 Jul 2008, Bridget Thomson McInnes wrote:
> >>>>
> >>>>> Hi Ted,
> >>>>>
> >>>>> I just downloaded the CuiTools from the webpage and got the same error.
> >>>>> I
> >>>>> will see why it is doing this!
> >>>>>
> >>>>> Thanks!
> >>>>>
> >>>>> Bridget
> >>>>>
> >>>>> On Wed, 23 Jul 2008, Ted Pedersen wrote:
> >>>>>
> >>>>>> Hi Bridget,
> >>>>>>
> >>>>>> I'm in the process of running the --mesh option again, this time just
> >>>>>> using adjustment and --mesh, as in...
> >>>>>>
> >>>>>> supervised-disambiguate.pl Demos/TDP.mm/adjustment.mm --mesh
> >>>>>> --directory ted-adjustment-mesh
> >>>>>>
> >>>>>> One thing I've noticed in the previous cases with --mesh is that the
> >>>>>> log directory is empty - which I guess means that no features were
> >>>>>> found, or something....then of course the ARFF files don't have any
> >>>>>> features in the them either, leading to the majority classifier...
> >>>>>>
> >>>>>> This isn't just specific to --mesh, but I do think it would be a good
> >>>>>> idea to issue a warning or possibly even an error when no features are
> >>>>>> found, just so the user doesn't end up getting a majority classifier
> >>>>>> without realizing it - unless I had been curious about the Mesh
> >>>>>> features I might not have noticed any of this, just because you do get
> >>>>>> results back even after finding no features. I think it might be ok to
> >>>>>> default to a majority classifier in this case, but we'd want the user
> >>>>>> to know that this has happened...
> >>>>>>
> >>>>>> My adjustment run just finished, so I've attached a zip file with the
> >>>>>> log, arff, weka and results directories...
> >>>>>>
> >>>>>> Thanks,
> >>>>>> Ted
> >>>>>>
> >>>>>> On Wed, Jul 23, 2008 at 2:33 PM, Bridget Thomson McInnes
> >>>>>> <bth...@cs...> wrote:
> >>>>>>>
> >>>>>>> Hi Ted,
> >>>>>>>
> >>>>>>> I am not certain. I am going to redownload the package, do a clean
> >>>>>>> install
> >>>>>>> and try it again. Hopefully I will be able to recreate it.
> >>>>>>>
> >>>>>>> Thanks!
> >>>>>>>
> >>>>>>> Bridget
> >>>>>>>
> >>>>>>> On Wed, 23 Jul 2008, Ted Pedersen wrote:
> >>>>>>>
> >>>>>>>> Hi Bridget,
> >>>>>>>>
> >>>>>>>> Thanks for this script - I ran it and it seems to give me back a fair
> >>>>>>>> number of results...so I seem to be able to access PubMed ok...
> >>>>>>>>
> >>>>>>>> marimba(4): perl get-mesh.pl 9337195
> >>>>>>>>      9337195 : *Birth Weight,Blood Glucose/metabolism,Blood
> >>>>>>>> Pressure,Brachial Artery/anatomy &
> >>>>>>>> histology/*physiology/ultrasonography,Cardiovascular
> >>>>>>>> Diseases/*epidemiology,Child,Cholesterol,
> >>>>>>>> LDL/blood,England,Female,Humans,Lipids/blood,Muscle, Smooth,
> >>>>>>>> Vascular/anatomy &
> >>>>>>>> histology/physiology/ultrasonography,Parity,Pregnancy,Regional Blood
> >>>>>>>> Flow,Risk Factors,Socioeconomic Factors,Tobacco Smoke
> >>>>>>>> Pollution,*Vasodilation
> >>>>>>>>
> >>>>>>>> What could I check next?
> >>>>>>>>
> >>>>>>>> Thanks,
> >>>>>>>> Ted
> >>>>>>>>
> >>>>>>>> On Wed, Jul 23, 2008 at 2:17 PM, Bridget Thomson McInnes
> >>>>>>>> <bth...@cs...> wrote:
> >>>>>>>>>
> >>>>>>>>> Hi Ted
> >>>>>>>>>
> >>>>>>>>> I attached a test script to check. It is called : get-msh.pl
> >>>>>>>>>
> >>>>>>>>> Here is an example run:
> >>>>>>>>>
> >>>>>>>>> bthomson@caesar (~) % perl get-msh.pl 9337195
> >>>>>>>>> 9337195 : *Birth Weight,Blood Glucose/metabolism,Blood
> >>>>>>>>> Pressure,Brachial
> >>>>>>>>> Artery/anatomy &
> >>>>>>>>> histology/*physiology/ultrasonography,Cardiovascular
> >>>>>>>>> Diseases/*epidemiology,Child,Cholesterol,
> >>>>>>>>> LDL/blood,England,Female,Humans,Lipids/blood,Muscle, Smooth,
> >>>>>>>>> Vascular/anatomy &
> >>>>>>>>> histology/physiology/ultrasonography,Parity,Pregnancy,Regional Blood
> >>>>>>>>> Flow,Risk Factors,Socioeconomic Factors,Tobacco Smoke
> >>>>>>>>> Pollution,*Vasodilation
> >>>>>>>>>
> >>>>>>>>>
> >>>>>>>>> This is the same result that I get on my computer at school and here
> >>>>>>>>> at
> >>>>>>>>> work.
> >>>>>>>>>
> >>>>>>>>> Thanks!
> >>>>>>>>>
> >>>>>>>>> Bridget
> >>>>>>>>>
> >>>>>>>>>
> >>>>>>>>> On Wed, 23 Jul 2008, Ted Pedersen wrote:
> >>>>>>>>>
> >>>>>>>>>> Hi Bridget,
> >>>>>>>>>>
> >>>>>>>>>> TDP.mm is just a copy of McInnesPC07.dir.mm from the Demos
> >>>>>>>>>> directory.
> >>>>>>>>>> Did you mean
> >>>>>>>>>> that, or the actual output?
> >>>>>>>>>>
> >>>>>>>>>> I do have an internet connection so I don't think that's the
> >>>>>>>>>> problem.
> >>>>>>>>>> How would I know if
> >>>>>>>>>> PubMed cut me off?
> >>>>>>>>>>
> >>>>>>>>>> Thanks!
> >>>>>>>>>> Ted
> >>>>>>>>>>
> >>>>>>>>>> On Wed, Jul 23, 2008 at 12:40 PM, Bridget Thomson McInnes
> >>>>>>>>>> <bth...@cs...> wrote:
> >>>>>>>>>>>
> >>>>>>>>>>> Hi Ted,
> >>>>>>>>>>>
> >>>>>>>>>>> I am not certain why this is happening. I don't have this problem.
> >>>>>>>>>>> The
> >>>>>>>>>>> mesh terms are obtained using the PubMed API. I can see two
> >>>>>>>>>>> potential
> >>>>>>>>>>> problems:
> >>>>>>>>>>>     1. No internet connection
> >>>>>>>>>>>             - which I will put in the documentation!
> >>>>>>>>>>>
> >>>>>>>>>>>     2. Do you think PubMed cut you off? They have done that to me
> >>>>>>>>>>>             before. They just start rejecting my queries if they
> >>>>>>>>>>>             think I have been using it to much. I have not quite
> >>>>>>>>>>>             determined what to much is yet. I will write a
> >>>>>>>>>>>             check in the program to make certain that something
> >>>>>>>>>>>             is coming back and if not error out.
> >>>>>>>>>>>
> >>>>>>>>>>> Otherwise I can't think of what it is. It isn't like using the
> >>>>>>>>>>> UMLSKS
> >>>>>>>>>>> API
> >>>>>>>>>>> where the ip address needs to be registered. I have only tested
> >>>>>>>>>>> this
> >>>>>>>>>>> inside NLM - my connection at the apartment goes in and out so I
> >>>>>>>>>>> haven't
> >>>>>>>>>>> been able to test this on my laptop.
> >>>>>>>>>>>
> >>>>>>>>>>> Could you send me your TDP.mm file?
> >>>>>>>>>>>
> >>>>>>>>>>> Thanks!
> >>>>>>>>>>>
> >>>>>>>>>>> Bridget
> >>>>>>>>>>>
> >>>>>>>>>>>
> >>>>>>>>>>> On Wed, 23 Jul 2008, Ted Pedersen wrote:
> >>>>>>>>>>>
> >>>>>>>>>>>> Hi Bridget,
> >>>>>>>>>>>>
> >>>>>>>>>>>> When using the Mesh option (--mesh) by itself, I seem to never
> >>>>>>>>>>>> get
> >>>>>>>>>>>> any
> >>>>>>>>>>>> features...
> >>>>>>>>>>>>
> >>>>>>>>>>>> My arff files all look something like this...
> >>>>>>>>>>>>
> >>>>>>>>>>>> @RELATION pressure
> >>>>>>>>>>>> @ATTRIBUTE Sense {M1,M2,M3,None}
> >>>>>>>>>>>> @DATA
> >>>>>>>>>>>> M1 % 97403834
> >>>>>>>>>>>> M1 % 98281278
> >>>>>>>>>>>> M1 % 98124304
> >>>>>>>>>>>>
> >>>>>>>>>>>> And so I end up getting a majority classifier...
> >>>>>>>>>>>>
> >>>>>>>>>>>> Is there something I am supposed to be doing to get the mesh
> >>>>>>>>>>>> features?
> >>>>>>>>>>>> I am just running like this...
> >>>>>>>>>>>>
> >>>>>>>>>>>> supervised-disambiguate.pl TDP.mm --mesh
> >>>>>>>>>>>>
> >>>>>>>>>>>> where TDP.mm is a directory with all the NLM-WSD data in .mm
> >>>>>>>>>>>> format
> >>>>>>>>>>>> (one file per word). All the files
> >>>>>>>>>>>> seem to be getting processed, and no errors are shown, but the
> >>>>>>>>>>>> results
> >>>>>>>>>>>> are pretty much just a majority
> >>>>>>>>>>>> classifier (due to lack of features...)
> >>>>>>>>>>>>
> >>>>>>>>>>>> Any idea on this?
> >>>>>>>>>>>>
> >>>>>>>>>>>> Thanks!
> >>>>>>>>>>>> Ted
> >>>>>>>>>>>>
> >>>>>>>>>>>> --
> >>>>>>>>>>>> Ted Pedersen
> >>>>>>>>>>>> http://www.d.umn.edu/~tpederse
> >>>>>>>>>>>>
> >>>>>>>>>>>
> >>>>>>>>>>
> >>>>>>>>>>
> >>>>>>>>>>
> >>>>>>>>>> --
> >>>>>>>>>> Ted Pedersen
> >>>>>>>>>> http://www.d.umn.edu/~tpederse
> >>>>>>>>>>
> >>>>>>>>
> >>>>>>>>
> >>>>>>>>
> >>>>>>>> --
> >>>>>>>> Ted Pedersen
> >>>>>>>> http://www.d.umn.edu/~tpederse
> >>>>>>>>
> >>>>>>>
> >>>>>>
> >>>>>>
> >>>>>>
> >>>>>> --
> >>>>>> Ted Pedersen
> >>>>>> http://www.d.umn.edu/~tpederse
> >>>>>>
> >>>>>
> >>>>>
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> >>>>> _______________________________________________
> >>>>> Cuitools-users mailing list
> >>>>> Cui...@li...
> >>>>> https://lists.sourceforge.net/lists/listinfo/cuitools-users
> >>>>>
> >>>>
> >>>
> >>>
> >>>
> >>> --
> >>> Ted Pedersen
> >>> http://www.d.umn.edu/~tpederse
> >>>
> >>
> >
> >
> >
> > --
> > Ted Pedersen
> > http://www.d.umn.edu/~tpederse
> >
>
>
>
> --
> Ted Pedersen
> http://www.d.umn.edu/~tpederse
>