Privacy-preserving machine learning has become critical for deploying artificial intelligence in sensitive domains such as healthcare, finance, and infrastructure monitoring. Homomorphic encryption (HE) enables secure inference on encrypted data. Despite its advantages, HE is not compatible with nonlinear activation functions found in machine learning models. Existing methods mitigate this problem by manually designing polynomial approximations for these activation functions. However, these functions do not account for the differences in dataset characteristics or model architecture. Furthermore, these functions are also limited to the accuracies of convolutional neural network (CNN) models. In this work, we propose an autonomous framework that selects polynomial activation functions tailored to each dataset and model. Using this framework, we analyze the interdependence between polynomial activation design and model architecture by evaluating several CNN ResNet and Vision Transformer models across multiple datasets. Experimental results demonstrate that the proposed framework generalizes across multiple architectures, including ResNet-18, ResNet-34, ResNet-50, ViT-S/16, ViT-B/16, and ViT-L/16. Across all datasets, transformer-based models maintain higher accuracy under polynomial approximation, while convolutional models exhibit increased degradation as task complexity grows. In addition, latency analysis reveals that the proposed CLS token based inference pipeline significantly reduces computational overhead by eliminating depth-dependent operations, shifting the primary cost to encryption and decryption. These findings demonstrate that the proposed method not only adapts polynomial activations across architectures, but also enables efficientencrypted inference through both activation design and pipeline optimization.

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