The remarkable success of machine learning (ML) in predictive tasks has led scientists to incorporate ML predictions as a core component of the scientific discovery pipeline. This was exemplified by the landmark achievement of AlphaFold (Jumper et al. (2021)). In this paper, we study how ML predictions can be safely used in statistical analysis of data towards scientific discovery. In particular, we follow the framework introduced by Angelopoulos et al. (2023). In this framework, we assume access to a small set of $n$ gold-standard labeled samples, a much larger set of $N$ unlabeled samples, and a ML model that can be used to impute the labels of the unlabeled data points. We introduce two new learning-augmented estimators: (1) Prediction-Augmented Residual Tree (PART), and (2) Prediction-Augmented Quadrature (PAQ). Both estimators have significant advantages over existing estimators like PPI and PPI++ introduced by Angelopoulos et al. (2023) and Angelopoulos et al. (2024), respectively. PART is a decision-tree based estimator built using a greedy criterion. We first characterize PART's asymptotic distribution and demonstrate how to construct valid confidence intervals. Then we show that PART outperforms existing methods in real-world datasets from ecology, astronomy, and census reports, among other domains. This leads to estimators with higher confidence, which is the result of using both the gold-standard samples and the machine learning predictions. Finally, we provide a formal proof of the advantage of PART by exploring PAQ, an estimation that arises when considering the limit of PART when the depth its tree grows to infinity. Under appropriate assumptions in the input data we show that the variance of PAQ shrinks at rate of $O(N^{-1} + n^{-4})$, improving significantly on the $O(N^{-1}+n^{-1})$ rate of existing methods.