I solved my own question as follow:
foreach ($categories as $cat) {
$category_explode = get_the_author_meta( 'Category', $user->ID );
//output 4,5,16
$cat_ex = explode(',',$category_explode);
?>
<label> <input type="checkbox" name="category[]" value="<?php echo $cat->cat_ID; ?>" <?php foreach ($cat_ex as $cat_expld) { if($cat->cat_ID == $cat_expld){echo'checked="checked"';} }?> /><span> <?php echo $cat->cat_name; ?>
</label>
<?php } ?>