2018 International Joint Conference on Neural Networks (IJCNN), 2018
We consider the problem in regression analysis of identifying subpopulations that exhibit differe... more We consider the problem in regression analysis of identifying subpopulations that exhibit different patterns of response, where each subpopulation requires a different underlying model. Unlike statistical cohorts, these subpopulations are not known a priori; thus, we refer to them as cadres. When the cadres and their associated models are interpretable, modeling leads to insights about the subpopulations and their associations with the regression target. We introduce a discriminative model that simultaneously learns cadre assignment and target-prediction rules. Sparsity-inducing priors are placed on the model parameters, under which independent feature selection is performed for both the cadre assignment and targetprediction processes. We learn models using adaptive step size stochastic gradient descent, and we assess cadre quality with bootstrapped sample analysis. We present simulated results showing that, when the true clustering rule does not depend on the entire set of features...
Journal of the American Society for Mass Spectrometry, Jan 30, 2017
The effects of oxygen addition on a helium-based flowing atmospheric pressure afterglow (FAPA) io... more The effects of oxygen addition on a helium-based flowing atmospheric pressure afterglow (FAPA) ionization source are explored. Small amounts of oxygen doped into the helium discharge gas resulted in an increase in abundance of protonated water clusters by at least three times. A corresponding increase in protonated analyte signal was also observed for small polar analytes, such as methanol and acetone. Meanwhile, most other reagent ions (e.g., O2(+·), NO(+), etc.) significantly decrease in abundance with even 0.1% v/v oxygen in the discharge gas. Interestingly, when analytes that contained aromatic constituents were subjected to a He:O2-FAPA, a unique (M + 3)(+) ion resulted, while molecular or protonated molecular ions were rarely detected. Exact-mass measurements revealed that these (M + 3)(+) ions correspond to (M - CH + O)(+), with the most likely structure being pyrylium. Presence of pyrylium-based ions was further confirmed by tandem mass spectrometry of the (M + 3)(+) ion com...
Proceedings of the National Academy of Sciences, 2005
The a priori prediction of protein adsorption behavior has been a long-standing goal in several f... more The a priori prediction of protein adsorption behavior has been a long-standing goal in several fields. In the present work, property-modeling techniques have been used for the prediction of protein adsorption thermodynamics in ion-exchange systems directly from crystal structure. Quantitative structure–property relationship models of protein isotherm parameters and Gibbs free energy changes in ion-exchange systems were generated by using a support vector machine regression technique. The predictive ability of the models was demonstrated for two test-set proteins not included in the model training set. Molecular descriptors selected during model generation were examined to gain insights into the important physicochemical factors influencing stoichiometry, equilibrium, steric effects, and binding affinity in protein ion-exchange systems. The a priori prediction of protein isotherm parameters can have direct implications for various ion-exchange processes. As proof of concept, a multi...
2018 International Joint Conference on Neural Networks (IJCNN), 2018
We consider the problem in regression analysis of identifying subpopulations that exhibit differe... more We consider the problem in regression analysis of identifying subpopulations that exhibit different patterns of response, where each subpopulation requires a different underlying model. Unlike statistical cohorts, these subpopulations are not known a priori; thus, we refer to them as cadres. When the cadres and their associated models are interpretable, modeling leads to insights about the subpopulations and their associations with the regression target. We introduce a discriminative model that simultaneously learns cadre assignment and target-prediction rules. Sparsity-inducing priors are placed on the model parameters, under which independent feature selection is performed for both the cadre assignment and targetprediction processes. We learn models using adaptive step size stochastic gradient descent, and we assess cadre quality with bootstrapped sample analysis. We present simulated results showing that, when the true clustering rule does not depend on the entire set of features...
Journal of the American Society for Mass Spectrometry, Jan 30, 2017
The effects of oxygen addition on a helium-based flowing atmospheric pressure afterglow (FAPA) io... more The effects of oxygen addition on a helium-based flowing atmospheric pressure afterglow (FAPA) ionization source are explored. Small amounts of oxygen doped into the helium discharge gas resulted in an increase in abundance of protonated water clusters by at least three times. A corresponding increase in protonated analyte signal was also observed for small polar analytes, such as methanol and acetone. Meanwhile, most other reagent ions (e.g., O2(+·), NO(+), etc.) significantly decrease in abundance with even 0.1% v/v oxygen in the discharge gas. Interestingly, when analytes that contained aromatic constituents were subjected to a He:O2-FAPA, a unique (M + 3)(+) ion resulted, while molecular or protonated molecular ions were rarely detected. Exact-mass measurements revealed that these (M + 3)(+) ions correspond to (M - CH + O)(+), with the most likely structure being pyrylium. Presence of pyrylium-based ions was further confirmed by tandem mass spectrometry of the (M + 3)(+) ion com...
Proceedings of the National Academy of Sciences, 2005
The a priori prediction of protein adsorption behavior has been a long-standing goal in several f... more The a priori prediction of protein adsorption behavior has been a long-standing goal in several fields. In the present work, property-modeling techniques have been used for the prediction of protein adsorption thermodynamics in ion-exchange systems directly from crystal structure. Quantitative structure–property relationship models of protein isotherm parameters and Gibbs free energy changes in ion-exchange systems were generated by using a support vector machine regression technique. The predictive ability of the models was demonstrated for two test-set proteins not included in the model training set. Molecular descriptors selected during model generation were examined to gain insights into the important physicochemical factors influencing stoichiometry, equilibrium, steric effects, and binding affinity in protein ion-exchange systems. The a priori prediction of protein isotherm parameters can have direct implications for various ion-exchange processes. As proof of concept, a multi...
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Papers by Curt Breneman