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The diffusion coefficient of heavy quarks in a deconfined medium is examined in this research using a deep convolutional neural network (CNN) that is trained with data from relativistic heavy ion collisions involving heavy flavor hadrons. The CNN is trained using observables such as the nuclear modification factor <inline-formula><math xmlns="http://www.w3.org/1998/Math/MathML" display="inline"><semantics><msub><mi>R</mi><mrow><mi>A</mi><mi>A</mi></mrow></msub></semantics></math></inline-formula> and the elliptic flow <inline-formula><math xmlns="http://www.w3.org/1998/Math/MathML" display="inline"><semantics><msub><mi>v</mi><mn>2</mn></msub></semantics></math></inline-formula> of non-prompt <inline-formula><math xmlns="http://www.w3.org/1998/Math/MathML" display="inline"><semantics><mrow><mi>J</mi><mo>/</mo><mi>ψ</mi></mrow></semantics></math></inline-formula> from the B-hadron decay in different centralities, where B meson evolutions are calculated using the Langevin equation and the instantaneous coalescence model. The CNN outputs the parameters, thereby characterizing the temperature and momentum dependence of the heavy quark diffusion coefficient. By inputting the experimental data of the non-prompt <inline-formula><math xmlns="http://www.w3.org/1998/Math/MathML" display="inline"><semantics><mrow><mi>J</mi><mo>/</mo><mi>ψ</mi></mrow></semantics></math></inline-formula><inline-formula><math xmlns="http://www.w3.org/1998/Math/MathML" display="inline"><semantics><mrow><mo>(</mo><msub><mi>R</mi><mrow><mi>A</mi><mi>A</mi></mrow></msub><mo>,</mo><msub><mi>v</mi><mn>2</mn></msub><mo>)</mo></mrow></semantics></math></inline-formula> from various collision centralities into multiple channels of a well-trained network, we derive the values of the diffusion coefficient parameters. Additionally, we evaluate the uncertainty in determining the diffusion coefficient by taking into account the uncertainties present in the experimental data <inline-formula><math xmlns="http://www.w3.org/1998/Math/MathML" display="inline"><semantics><mrow><mo>(</mo><msub><mi>R</mi><mrow><mi>A</mi><mi>A</mi></mrow></msub><mo>,</mo><msub><mi>v</mi><mn>2</mn></msub><mo>)</mo></mrow></semantics></math></inline-formula>, which serve as inputs to the deep neural network.