Mixture model with logistic regression

8 messages 6 people Latest: Feb 21, 2016

Mixture model with logistic regression

From: Mark Sale Date: February 19, 2016 technical
Has anyone every tried to use a mixture model with logistic regression? I have data on a AE in several hundred patients, measured multiple times (10-20 times per patient). Examining the data it is clear that, independent of drug concentration, there is very wide distribution of this AE, 68% of the patients never have the AE, 25% have it about 20% of the time and the rest have it pretty much continuously, regardless of drug concentration. (in ordinary logistic regression, just glm in R, there is also a nice concentration effect on the AE in addition). Running the usual logistic model, not surprisingly, I get a really big ETA on the intercept, with 68% of the people having ETA small negative, 25% ETA ~ 1 and 7% ETA ~ 10. No covariates seem particularly predictive of the post hoc ETA. I thought I could use a mixture model, with 3 modes, but it refused to do that, giving me essentially 0% in the 2nd and 3rd distribution, still with the really large OMEGA for the intercept. Even when I FIX the OMEGA to a reasonable number, I still get essentially no one in the 2nd and 3rd distribution. I tried fixing the fraction in the 2nd and 3rd distribution (and OMEGA), and it still gave me a very small difference in the intercept for the 2nd and 3rd populations. Is there an issue with using mixture models with logistic regression? I'm just using FOCE, Laplacian, without interaction, and LIKE. Any ideas? Mark Mark Sale M.D. Vice President, Modeling and Simulation Nuventra, Inc. (tm) 2525 Meridian Parkway, Suite 280 Research Triangle Park, NC 27713 Office (919)-973-0383 [email protected]<[email protected]> http://www.nuventra.com
Use of mixture model may not be suitable here, if the underlying distribution of eta's for the different subgroups is not normally distributed. Based on the description, it looks like you have 3 degenerate eta distributions(ETA ~0 for no AE; ETA ~1 for 25% AE and ETA ~10 for 7% with all AE), which violates the normality assumption. Upon quick search, I came across this article, where they have described almost a similar situation as yours. They have used a two part mixture distribution to take care of the large proportions of the subjects with no AE. Hope it is helpful. http://www.ncbi.nlm.nih.gov/pubmed/14977163 Kowalski, Kenneth G., Lynn McFadyen, Matthew M. Hutmacher, Bill Frame, and Raymond Miller. "A Two-Part Mixture Model for Longitudinal Adverse Event Severity Data." Journal of Pharmacokinetics and Pharmacodynamics 30, no. 5 (October 2003): 315-36. Thanks. Mathangi Gopalakrishnan, MS, PhD Research Assistant Professor Center for Translational Medicine (CTM) School of Pharmacy, UMB Ph: 410-706-7842 http://www.ctm.umaryland.edu/
Quoted reply history
From: [email protected] [mailto:[email protected]] On Behalf Of Mark Sale Sent: Friday, February 19, 2016 5:30 PM To: [email protected] Subject: [NMusers] Mixture model with logistic regression Has anyone every tried to use a mixture model with logistic regression? I have data on a AE in several hundred patients, measured multiple times (10-20 times per patient). Examining the data it is clear that, independent of drug concentration, there is very wide distribution of this AE, 68% of the patients never have the AE, 25% have it about 20% of the time and the rest have it pretty much continuously, regardless of drug concentration. (in ordinary logistic regression, just glm in R, there is also a nice concentration effect on the AE in addition). Running the usual logistic model, not surprisingly, I get a really big ETA on the intercept, with 68% of the people having ETA small negative, 25% ETA ~ 1 and 7% ETA ~ 10. No covariates seem particularly predictive of the post hoc ETA. I thought I could use a mixture model, with 3 modes, but it refused to do that, giving me essentially 0% in the 2nd and 3rd distribution, still with the really large OMEGA for the intercept. Even when I FIX the OMEGA to a reasonable number, I still get essentially no one in the 2nd and 3rd distribution. I tried fixing the fraction in the 2nd and 3rd distribution (and OMEGA), and it still gave me a very small difference in the intercept for the 2nd and 3rd populations. Is there an issue with using mixture models with logistic regression? I'm just using FOCE, Laplacian, without interaction, and LIKE. Any ideas? Mark Mark Sale M.D. Vice President, Modeling and Simulation Nuventra, Inc. (tm) 2525 Meridian Parkway, Suite 280 Research Triangle Park, NC 27713 Office (919)-973-0383 [email protected]<[email protected]> http://www.nuventra.com

RE: Mixture model with logistic regression

From: Bob Leary Date: February 20, 2016 technical
This sounds like a good case for a nonparametric method - if you use the one in NONMEM, you might try expanding Omega to counter shrinkage. The versions in USC*PACK and PHOENIX NLME optimize over both support point positions and probabilities, so this is not necessary with those methods.
Quoted reply history
________________________________ From: [email protected] [[email protected]] on behalf of Mark Sale [[email protected]] Sent: Friday, February 19, 2016 4:30 PM To: [email protected] Subject: [NMusers] Mixture model with logistic regression Has anyone every tried to use a mixture model with logistic regression? I have data on a AE in several hundred patients, measured multiple times (10-20 times per patient). Examining the data it is clear that, independent of drug concentration, there is very wide distribution of this AE, 68% of the patients never have the AE, 25% have it about 20% of the time and the rest have it pretty much continuously, regardless of drug concentration. (in ordinary logistic regression, just glm in R, there is also a nice concentration effect on the AE in addition). Running the usual logistic model, not surprisingly, I get a really big ETA on the intercept, with 68% of the people having ETA small negative, 25% ETA ~ 1 and 7% ETA ~ 10. No covariates seem particularly predictive of the post hoc ETA. I thought I could use a mixture model, with 3 modes, but it refused to do that, giving me essentially 0% in the 2nd and 3rd distribution, still with the really large OMEGA for the intercept. Even when I FIX the OMEGA to a reasonable number, I still get essentially no one in the 2nd and 3rd distribution. I tried fixing the fraction in the 2nd and 3rd distribution (and OMEGA), and it still gave me a very small difference in the intercept for the 2nd and 3rd populations. Is there an issue with using mixture models with logistic regression? I'm just using FOCE, Laplacian, without interaction, and LIKE. Any ideas? Mark Mark Sale M.D. Vice President, Modeling and Simulation Nuventra, Inc. ™ 2525 Meridian Parkway, Suite 280 Research Triangle Park, NC 27713 Office (919)-973-0383 [email protected]<UrlBlockedError.aspx> http://www.nuventra.com

Re: Mixture model with logistic regression

From: Mark Sale Date: February 20, 2016 technical
Bob, That certainly makes sense, but that options seems to not be available in NONMEM, using LIKE seems to require using FOCE LAPLACE LIKELIHOOD This is designed mainly, but not exclusively, for use with non- continuous observed responses ("odd-type data"). Indicates that Y (with NM-TRAN abbreviated code) or F (with a user-supplied PRED or ERROR code) will be set to a (conditional) likelihood. Upon simulation it will be ignored, and the DV data item will be set directly to the simulated value in abbreviated or user code. Also etas, if any, are understood to be population etas. Epsilon variables and the $SIGMA record may not be used. The L2 data item may not be used. The CONTR and CCONTR options of the $SUB- ROUTINES record may not be used. NONMEM cannot obtain the ini- tial estimate for omega. If the data are population, and MAXE- VALS=0 is not coded, then METHOD=1 LAPLACE is required. Compare with PREDICTION option. Mark Sale M.D. Vice President, Modeling and Simulation Nuventra, Inc. ™ 2525 Meridian Parkway, Suite 280 Research Triangle Park, NC 27713 Office (919)-973-0383 [email protected]<[email protected]> http://www.nuventra.com Empower your Pipeline CONFIDENTIALITY NOTICE The information in this transmittal (including attachments, if any) may be privileged and confidential and is intended only for the recipient(s) listed above. Any review, use, disclosure, distribution or copying of this transmittal, in any form, is prohibited except by or on behalf of the intended recipient(s). If you have received this transmittal in error, please notify me immediately by reply email and destroy all copies of the transmittal.
Quoted reply history
________________________________ From: Bob Leary <[email protected]> Sent: Saturday, February 20, 2016 8:45 AM To: Mark Sale; [email protected] Subject: RE: Mixture model with logistic regression This sounds like a good case for a nonparametric method - if you use the one in NONMEM, you might try expanding Omega to counter shrinkage. The versions in USC*PACK and PHOENIX NLME optimize over both support point positions and probabilities, so this is not necessary with those methods. ________________________________ From: [email protected] [[email protected]] on behalf of Mark Sale [[email protected]] Sent: Friday, February 19, 2016 4:30 PM To: [email protected] Subject: [NMusers] Mixture model with logistic regression Has anyone every tried to use a mixture model with logistic regression? I have data on a AE in several hundred patients, measured multiple times (10-20 times per patient). Examining the data it is clear that, independent of drug concentration, there is very wide distribution of this AE, 68% of the patients never have the AE, 25% have it about 20% of the time and the rest have it pretty much continuously, regardless of drug concentration. (in ordinary logistic regression, just glm in R, there is also a nice concentration effect on the AE in addition). Running the usual logistic model, not surprisingly, I get a really big ETA on the intercept, with 68% of the people having ETA small negative, 25% ETA ~ 1 and 7% ETA ~ 10. No covariates seem particularly predictive of the post hoc ETA. I thought I could use a mixture model, with 3 modes, but it refused to do that, giving me essentially 0% in the 2nd and 3rd distribution, still with the really large OMEGA for the intercept. Even when I FIX the OMEGA to a reasonable number, I still get essentially no one in the 2nd and 3rd distribution. I tried fixing the fraction in the 2nd and 3rd distribution (and OMEGA), and it still gave me a very small difference in the intercept for the 2nd and 3rd populations. Is there an issue with using mixture models with logistic regression? I'm just using FOCE, Laplacian, without interaction, and LIKE. Any ideas? Mark Mark Sale M.D. Vice President, Modeling and Simulation Nuventra, Inc. ™ 2525 Meridian Parkway, Suite 280 Research Triangle Park, NC 27713 Office (919)-973-0383 [email protected]<UrlBlockedError.aspx> http://www.nuventra.com

Re: Mixture model with logistic regression

From: Matts Kågedal Date: February 20, 2016 technical
Hi Mark, The pattern you see in the posthocs could possibly be a shrinkage phenomenon. I.e. patients with AE most of the time will have the same ETA, while patients with no AE will have the same ETA and there will be a third group in between. If shrinkage is causing this, you should not expect any improvement with a mixture model. Before you reject your original model I would therefore also evaluate it by simulation and re-estimation. I think it is quite possible that you will retreive a similar pattern in the posthocs even when you simulate based on a normal distribution. Best, Matts Kågedal Pharmacometrics, Genentech.
Quoted reply history
On Fri, Feb 19, 2016 at 2:30 PM, Mark Sale <[email protected]> wrote: > Has anyone every tried to use a mixture model with logistic regression? I > have data on a AE in several hundred patients, measured multiple times > (10-20 times per patient). Examining the data it is clear that, > independent of drug concentration, there is very wide distribution of this > AE, 68% of the patients never have the AE, 25% have it about 20% of the > time and the rest have it pretty much continuously, regardless of > drug concentration. (in ordinary logistic regression, just glm in R, there > is also a nice concentration effect on the AE in addition). Running the > usual logistic model, not surprisingly, I get a really big ETA on the > intercept, with 68% of the people having ETA small negative, 25% ETA ~ 1 > and 7% ETA ~ 10. No covariates seem particularly predictive of the post hoc > ETA. I thought I could use a mixture model, with 3 modes, but it refused > to do that, giving me essentially 0% in the 2nd and 3rd distribution, still > with the really large OMEGA for the intercept. Even when I FIX the OMEGA > to a reasonable number, I still get essentially no one in the 2nd and 3rd > distribution. I tried fixing the fraction in the 2nd and 3rd distribution > (and OMEGA), and it still gave me a very small difference in the intercept > for the 2nd and 3rd populations. > > Is there an issue with using mixture models with logistic regression? I'm > just using FOCE, Laplacian, without interaction, and LIKE. > > > > > Any ideas? > > > Mark > > > > Mark Sale M.D. > > Vice President, Modeling and Simulation > > Nuventra, Inc. ™ > > 2525 Meridian Parkway, Suite 280 > > Research Triangle Park, NC 27713 > > Office (919)-973-0383 > > [email protected] http://[email protected] > > www.nuventra.com > > > >
Hi Mark, Is it indeed a logistical model or is it an ordered categorical? I assume you refer to the latter. Not sure how you get your second category otherwise. Anyway, to me it reads like you are trying to have the mixture model describe exactly what the omega is trying to describe. Perhaps you could drop the omega all together? (or fix to a small value) I also like Bob's suggestion, I would go for it ($NPAR!). Hope this helps, Jeroen http://pd-value.com [email protected] @PD_value +31 6 23118438 -- More value out of your data! Op 20-02-16 om 21:01 schreef Mark Sale: > Matts, > > Thanks for your insights. But, the issue isn't the post hoc values. With the mixture model the OMEGA on the intercept is huge (680), and the entire population is in the low intercept value group (Intercept = -11). Then to accommodate the patients with frequent AEs, it assigns a (post hoc) ETA of +15, giving an individual value for intercept of 6 (and a probability of the AE of ~1, as it should. My question is whey does it refuse to simply put those 8% of the patients in a sub population with intercept = 6, ETA=0. rather than saying the expected value is -11, with ETA = +15. Even when I fix the fractions in the subpopulations for the observed values, and fix OMEGA to a small, reasonable value, and fix the intercept values for the 3 populations to reasonable values it will still do this. The only thing that has worked is to assign each subject to the apparent population in the data set. > > Mark > > Mark Sale M.D. > > Vice President, Modeling and Simulation > > Nuventra, Inc. ™ > > 2525 Meridian Parkway, Suite 280 > > Research Triangle Park, NC 27713 > > Office (919)-973-0383 > > [email protected] <[email protected]> > > www.nuventra.com http://www.nuventra.com > > */ > /* > > */Empower your Pipeline/* > > CONFIDENTIALITY NOTICE The information in this transmittal (including attachments, if any) may be privileged and confidential and is intended only for the recipient(s) listed above. Any review, use, disclosure, distribution or copying of this transmittal, in any form, is prohibited except by or on behalf of the intended recipient(s). If you have received this transmittal in error, please notify me immediately by reply email and destroy all copies of the transmittal. > > ------------------------------------------------------------------------ > *From:* Matts Kågedal <[email protected]> > *Sent:* Saturday, February 20, 2016 2:44 PM > *To:* Mark Sale > *Cc:* [email protected] > *Subject:* Re: [NMusers] Mixture model with logistic regression > Hi Mark, > > The pattern you see in the posthocs could possibly be a shrinkage phenomenon. I.e. patients with AE most of the time will have the same ETA, while patients with no AE will have the same ETA and there will be a third group in between. If shrinkage is causing this, you should not expect any improvement with a mixture model. Before you reject your original model I would therefore also evaluate it by simulation and re-estimation. I think it is quite possible that you will retreive a similar pattern in the posthocs even when you simulate based on a normal distribution. > > Best, > Matts Kågedal > Pharmacometrics, Genentech. >
Quoted reply history
> On Fri, Feb 19, 2016 at 2:30 PM, Mark Sale < [email protected] < mailto: [email protected] >> wrote: > > Has anyone every tried to use a mixture model with logistic > regression? I have data on a AE in several hundred patients, > measured multiple times (10-20 times per patient). Examining the > data it is clear that, independent of drug concentration, there is > very wide distribution of this AE, 68% of the patients never have > the AE, 25% have it about 20% of the time and the rest have it > pretty much continuously, regardless of drug concentration. (in > ordinary logistic regression, just glm in R, there is also a nice > concentration effect on the AE in addition). Running the usual > logistic model, not surprisingly, I get a really big ETA on the > intercept, with 68% of the people having ETA small negative, 25% > ETA ~ 1 and 7% ETA ~ 10. No covariates seem particularly > predictive of the post hoc ETA. I thought I could use a mixture > model, with 3 modes, but it refused to do that, giving me > essentially 0% in the 2nd and 3rd distribution, still with the > really large OMEGA for the intercept. Even when I FIX the OMEGA > to a reasonable number, I still get essentially no one in the 2nd > and 3rd distribution. I tried fixing the fraction in the 2nd and > 3rd distribution (and OMEGA), and it still gave me a very small > difference in the intercept for the 2nd and 3rd populations. > > Is there an issue with using mixture models with logistic > regression? I'm just using FOCE, Laplacian, without interaction, > and LIKE. > > Any ideas? > > Mark > > Mark Sale M.D. > > Vice President, Modeling and Simulation > > Nuventra, Inc. ™ > > 2525 Meridian Parkway, Suite 280 > > Research Triangle Park, NC 27713 > > Office (919)-973-0383 <tel:%28919%29-973-0383> > > [email protected] http://[email protected] > > www.nuventra.com http://www.nuventra.com

Re: Mixture model with logistic regression

From: Gerry Sheng Date: February 20, 2016 technical
Hi Mark, My first suggestion is you can start from simpler mixture model (e.g. 2 distributions) and only focus on those have AEs. 68% patients without AE is a big disturbance to intercept. Only negative infinity of intercept in logistic model can give a probability=0. Secondly, you can try to use SAEM method with mu reference. Based on my own experience, FOCE method is not as powerful as SAEM in likelihood estimations. Good luck. BW, Yucheng Sheng UCL School of Pharmacy 29-39 Brunswick Square London WC1N 1AX Email. [email protected]
Quoted reply history
On 19 February 2016 at 22:30, Mark Sale <[email protected]> wrote: > Has anyone every tried to use a mixture model with logistic regression? I > have data on a AE in several hundred patients, measured multiple times > (10-20 times per patient). Examining the data it is clear that, > independent of drug concentration, there is very wide distribution of this > AE, 68% of the patients never have the AE, 25% have it about 20% of the > time and the rest have it pretty much continuously, regardless of > drug concentration. (in ordinary logistic regression, just glm in R, there > is also a nice concentration effect on the AE in addition). Running the > usual logistic model, not surprisingly, I get a really big ETA on the > intercept, with 68% of the people having ETA small negative, 25% ETA ~ 1 > and 7% ETA ~ 10. No covariates seem particularly predictive of the post hoc > ETA. I thought I could use a mixture model, with 3 modes, but it refused > to do that, giving me essentially 0% in the 2nd and 3rd distribution, still > with the really large OMEGA for the intercept. Even when I FIX the OMEGA > to a reasonable number, I still get essentially no one in the 2nd and 3rd > distribution. I tried fixing the fraction in the 2nd and 3rd distribution > (and OMEGA), and it still gave me a very small difference in the intercept > for the 2nd and 3rd populations. > > Is there an issue with using mixture models with logistic regression? I'm > just using FOCE, Laplacian, without interaction, and LIKE. > > > > > Any ideas? > > > Mark > > > > Mark Sale M.D. > > Vice President, Modeling and Simulation > > Nuventra, Inc. ™ > > 2525 Meridian Parkway, Suite 280 > > Research Triangle Park, NC 27713 > > Office (919)-973-0383 > > [email protected] http://[email protected] > > www.nuventra.com > > > >

Re: Mixture model with logistic regression

From: Mark Sale Date: February 21, 2016 technical
Kudos to Jeroen, who solved this for me, needed the NOINTER option on $EST, then you can use SAEM, which gave a reasonable answer, unlike FOCE. Mark Mark Sale M.D. Vice President, Modeling and Simulation Nuventra, Inc. ™ 2525 Meridian Parkway, Suite 280 Research Triangle Park, NC 27713 Office (919)-973-0383 [email protected]<[email protected]> http://www.nuventra.com Empower your Pipeline CONFIDENTIALITY NOTICE The information in this transmittal (including attachments, if any) may be privileged and confidential and is intended only for the recipient(s) listed above. Any review, use, disclosure, distribution or copying of this transmittal, in any form, is prohibited except by or on behalf of the intended recipient(s). If you have received this transmittal in error, please notify me immediately by reply email and destroy all copies of the transmittal.
Quoted reply history
________________________________ From: Jeroen Elassaiss-Schaap (PD-value B.V.) <[email protected]> Sent: Saturday, February 20, 2016 4:35 PM To: Mark Sale Cc: [email protected] Subject: Re: [NMusers] Mixture model with logistic regression Hi Mark, Is it indeed a logistical model or is it an ordered categorical? I assume you refer to the latter. Not sure how you get your second category otherwise. Anyway, to me it reads like you are trying to have the mixture model describe exactly what the omega is trying to describe. Perhaps you could drop the omega all together? (or fix to a small value) I also like Bob's suggestion, I would go for it ($NPAR!). Hope this helps, Jeroen http://pd-value.com [email protected]<mailto:[email protected]> @PD_value +31 6 23118438 -- More value out of your data! Op 20-02-16 om 21:01 schreef Mark Sale: Matts, Thanks for your insights. But, the issue isn't the post hoc values. With the mixture model the OMEGA on the intercept is huge (680), and the entire population is in the low intercept value group (Intercept = -11). Then to accommodate the patients with frequent AEs, it assigns a (post hoc) ETA of +15, giving an individual value for intercept of 6 (and a probability of the AE of ~1, as it should. My question is whey does it refuse to simply put those 8% of the patients in a sub population with intercept = 6, ETA=0. rather than saying the expected value is -11, with ETA = +15. Even when I fix the fractions in the subpopulations for the observed values, and fix OMEGA to a small, reasonable value, and fix the intercept values for the 3 populations to reasonable values it will still do this. The only thing that has worked is to assign each subject to the apparent population in the data set. Mark Mark Sale M.D. Vice President, Modeling and Simulation Nuventra, Inc. ™ 2525 Meridian Parkway, Suite 280 Research Triangle Park, NC 27713 Office (919)-973-0383 [email protected]<[email protected]> http://www.nuventra.com Empower your Pipeline CONFIDENTIALITY NOTICE The information in this transmittal (including attachments, if any) may be privileged and confidential and is intended only for the recipient(s) listed above. Any review, use, disclosure, distribution or copying of this transmittal, in any form, is prohibited except by or on behalf of the intended recipient(s). If you have received this transmittal in error, please notify me immediately by reply email and destroy all copies of the transmittal. ________________________________ From: Matts Kågedal <[email protected]><mailto:[email protected]> Sent: Saturday, February 20, 2016 2:44 PM To: Mark Sale Cc: [email protected]<mailto:[email protected]> Subject: Re: [NMusers] Mixture model with logistic regression Hi Mark, The pattern you see in the posthocs could possibly be a shrinkage phenomenon. I.e. patients with AE most of the time will have the same ETA, while patients with no AE will have the same ETA and there will be a third group in between. If shrinkage is causing this, you should not expect any improvement with a mixture model. Before you reject your original model I would therefore also evaluate it by simulation and re-estimation. I think it is quite possible that you will retreive a similar pattern in the posthocs even when you simulate based on a normal distribution. Best, Matts Kågedal Pharmacometrics, Genentech. On Fri, Feb 19, 2016 at 2:30 PM, Mark Sale <[email protected]<mailto:[email protected]>> wrote: Has anyone every tried to use a mixture model with logistic regression? I have data on a AE in several hundred patients, measured multiple times (10-20 times per patient). Examining the data it is clear that, independent of drug concentration, there is very wide distribution of this AE, 68% of the patients never have the AE, 25% have it about 20% of the time and the rest have it pretty much continuously, regardless of drug concentration. (in ordinary logistic regression, just glm in R, there is also a nice concentration effect on the AE in addition). Running the usual logistic model, not surprisingly, I get a really big ETA on the intercept, with 68% of the people having ETA small negative, 25% ETA ~ 1 and 7% ETA ~ 10. No covariates seem particularly predictive of the post hoc ETA. I thought I could use a mixture model, with 3 modes, but it refused to do that, giving me essentially 0% in the 2nd and 3rd distribution, still with the really large OMEGA for the intercept. Even when I FIX the OMEGA to a reasonable number, I still get essentially no one in the 2nd and 3rd distribution. I tried fixing the fraction in the 2nd and 3rd distribution (and OMEGA), and it still gave me a very small difference in the intercept for the 2nd and 3rd populations. Is there an issue with using mixture models with logistic regression? I'm just using FOCE, Laplacian, without interaction, and LIKE. Any ideas? Mark Mark Sale M.D. Vice President, Modeling and Simulation Nuventra, Inc. ™ 2525 Meridian Parkway, Suite 280 Research Triangle Park, NC 27713 Office (919)-973-0383<tel:%28919%29-973-0383> [email http://[email protected] http://www.nuventra.com