Accurate prediction of structural failure modes under seismic excitations is essential for seismic risk and resilience assessment. Traditional simulation-based approaches often result in imbalanced datasets dominated by non-failure or frequently observed failure scenarios, limiting the effectiveness in machine learning-based prediction. To address this challenge, this study proposes a framework for constructing balanced datasets that include distinct failure modes. The framework consists of three key steps. First, critical ground motion features (GMFs) are identified to effectively represent ground motion time histories. Second, an adaptive algorithm is employed to estimate the probability densities of various failure domains in the space of critical GMFs and structural parameters. Third, samples generated from these probability densities are transformed into ground motion time histories by using a scaling factor optimization process. A balanced dataset is constructed by performing nonlinear response history analyses on structural systems with parameters matching the generated samples, subjected to corresponding transformed ground motion time histories. Deep neural network models are trained on balanced and imbalanced datasets to highlight the importance of dataset balancing. To further evaluate the framework's applicability, numerical investigations are conducted using two different structural models subjected to recorded and synthetic ground motions. The results demonstrate the framework's robustness and effectiveness in addressing dataset imbalance and improving machine learning performance in seismic failure mode prediction.