A pathway EM-algorithm for estimating vaccine efficacy with a non-monotone validation set.

Here, we consider time-to-event data where individuals can experience two or more types of events that are not distinguishable from one another without further confirmation, perhaps by laboratory test. The event type of primary interest can occur only once. The other types of events can recur. If the type of a portion of the events is identified, this forms a validation set. However, even if a random sample of events are tested, confirmations can be missing nonmonotonically, creating uncertainty about whether an individual is still at risk for the event of interest. For example, in a study to estimate efficacy of an influenza vaccine, an individual may experience a sequence of symptomatic respiratory illnesses caused by various pathogens over the season. Often only a limited number of these episodes are confirmed in the laboratory to be influenza-related or not. We propose two novel methods to estimate covariate effects in this survival setting, and subsequently vaccine efficacy. The first is a pathway expectation-maximization (EM) algorithm that takes into account all pathways of event types in an individual compatible with that individual's test outcomes. The pathway EM iteratively estimates baseline hazards that are used to weight possible event types. The second method is a non-iterative pathway piecewise validation method that does not estimate the baseline hazards. These methods are compared with a previous simpler method. Simulation studies suggest mean squared error is lower in the efficacy estimates when the baseline hazards are estimated, especially at higher hazard rates. We use the pathway EM-algorithm to reevaluate the efficacy of a trivalent live-attenuated influenza vaccine during the 2003-2004 influenza season in Temple-Belton, Texas, and compare our results with a previously published analysis.