We develop a novel debiased machine learning (DML) estimator to analyze count data, which are common in clinical or biomedical studies. Specifically, we estimate the effect of a binary treatment on count outcomes using a partially linear Poisson model. A key advantage of this model is that it represents the complex covariate structure through a nuisance function, which is estimated flexibly using neural networks. We use a Neyman-orthogonal score function to construct the estimator, reducing its sensitivity to errors in estimating the nuisance function. Cross-fitting is used to mitigate overfitting bias in neural networks. Under mild regularity conditions, this DML estimator is asymptotically normal with root-$n$ convergence. We derive a closed-form variance estimator and construct a Wald confidence interval for the treatment effect. Extensive simulations demonstrate that the proposed estimator reduces bias and root mean square error compared with the generalized linear model and the augmented inverse probability weighting (AIPW) estimator in most settings, while achieving a coverage probability near the nominal level. The proposed procedure is implemented in the R package $\texttt{PoissonDML}$. We apply our approach to a synthetic HIV cohort data to investigate the effect of treatment on AIDS-defining event counts of 7,141 analyzed patients. Our approach provides practical and valid estimation and inference for treatment effects under the partially linear Poisson model while combining modern machine learning methods to estimate complex covariate structures.

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