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How to change IEEEtran \IEEEauthorrefmark to numbered style 1, 2, 3... instead of the star and dagger marks and make the author affiliation as footnote in the first page?

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For the first question, you need to completely redefine \IEEEauthorrefmark:

\DeclareRobustCommand*{\IEEEauthorrefmark}[1]{%
  \raisebox{0pt}[0pt][0pt]{\textsup‌​erscript{\footnotesize\ensuremath{#1}}}}
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