1. A computer-implemented apparatus for controlling a process based on measured physical attributes, comprising: a non-transitory computer-readable storage medium having data structures for storing: (a) manifest variables based on said measured physical attributes; (b) latent variables representing causally related attributes associated with said manifest variables, the latent variables including predictor latent variables and dependent latent variables, wherein the dependent latent variables may be expressed as a linear combination of at least one predictor latent variables; (c) model specification parameters including a path structure parameter indicating causal path attributes to express the causal relationship between the predictor latent variables and the dependent latent variables and a value-based parameter indicating prediction priorities associated with weights of the dependent latent variables with respect to the predictor latent variables; a non-transitory computer-readable storage medium having encoded therein an initial run module that operates upon said data structures to provide estimates of weights associated with said latent variables; said initial run module providing estimates of weights of manifest variables with respect to latent variables by employing a computer-implemented value-based weighting partial least squares process employing an inside approximation weighting scheme utilizing the value based parameter thereby allowing optimization of each latent variable according to its own prediction priorities; the non-transitory computer-readable storage medium having encoded therein a final run module using said estimated weights and said manifest variables to calculate latent variable scores, wherein the latent variable scores are defined as weighted averages of manifest variables; said final run module employing a computer implemented patient partial least squares regression process that operates to calculate the path coefficients between predictor latent variables and dependent latent variables using the latent variable scores and path structure parameter; said final run module providing control parameter selections for controlling said process, where the control parameters are selected using the path coefficients associated with said latent variables.