This paper proposes an end-to-end convolutional selective autoencoder approach for early detection of combustion instabilities using rapidly arriving flame image frames. The instabilities arising in combustion processes cause significant deterioration and safety issues in various human-engineered systems such as land and air based gas turbine engines. These properties are described as self-sustaining, large amplitude pressure oscillations and show varying spatial scales periodic coherent vortex structure shedding. However, such instability is extremely difficult to detect before a combustion process becomes completely unstable due to its sudden (bifurcation-type) nature. In this context, an autoencoder is trained to selectively mask stable flame and allow unstable flame image frames. In that process, the model learns to identify and extract rich descriptive and explanatory flame shape features. With such a training scheme, the selective autoencoder is shown to be able to detect subtle instability features as a combustion process makes transition from stable to unstable region. As a consequence, the deep learning tool-chain can perform as an early detection framework for combustion instabilities that will have a transformative impact on the safety and performance of modern engines.