MySQL co-occurences from a link table (example treats docs as binarised vector of skills)

cooc.sql

CREATE TEMPORARY TABLE tmp_skills_a
PRIMARY key doc_id
SELECT doc_id, skill_id 
FROM skills_link_table 
GROUP BY doc_id, skill_id;

CREATE TEMPORARY TABLE tmp_skills_b
PRIMARY key doc_id
SELECT doc_id, skill_id 
FROM skills_link_table 
GROUP BY doc_id, skill_id;

SELECT skill_a, skill_b, COUNT(*) cnt 
FROM (SELECT a.skill_id AS skill_a, b.skill_id AS skill_b 
      FROM tmp_skills_a a 
      JOIN tmp_skills_b b ON a.doc_id = b.doc_id 
      WHERE a.skill_id > b.skill_id) t 
GROUP BY skill_a, skill_b;