Performance can be increased by correct indexes in table yarpp_related_cache. The table has a multicolumn index created as "PRIMARY KEY ( score , date , reference_ID , ID )". MySQL cannot use such index in most of SELECTs, example:
# Query_time: 0.017838 Lock_time: 0.000034 Rows_sent: 0 Rows_examined: 100543 select distinct reference_ID from wp_yarpp_related_cache where ID = 43287;
Single column indexes 'reference_ID' and 'ID' are necessary for such requests.