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Thermoelectric coolers (TECs) offer a promising solution for direct cooling of local hotspots and active thermal management in advanced electronic systems. However, TECs present significant trade-offs among spatial cooling, heating, and power consumption. The optimization of TECs requires extensive simulations, which are impractical for managing actual systems with multiple hotspots under spatial and temporal variations. In this study, we present a novel machine learning-assisted optimization algorithm for thermoelectric coolers that can achieve global optimal temperature by individually controlling TEC units based on real-time multi-hotspot conditions across the entire domain. We train a convolutional neural network with a combination of the inception module and multi-task learning approach to comprehend the coupled thermal-electrical physics underlying the system and attain accurate predictions for both temperature and power consumption with and without TECs. Due to the intricate interaction among passive thermal gradient, Peltier effect and Joule effect, a local optimal TEC control experiences spatial temperature trade-off which may not lead to a global optimal solution. To address this issue, we develop a backtracking-based optimization algorithm using the machine learning model to iterate all possible TEC assignments for attaining global optimal solutions. For any m × n matrix with NHS hotspots (n, m ≤ 10, 1 ≤ NHS ≤ 20), our algorithm is capable of providing 52.4% peak temperature reduction and its corresponding TEC array control within an average of 1.64 s while iterating through tens of temperature predictions behind-the-scenes. This represents a speed increase of over three orders of magnitude compared to traditional finite element method strategies which take approximately 27 min. [ABSTRACT FROM AUTHOR]