This volume constitutes the refereed proceedings of the three workshops held at the 31st International Conference on Database and Expert Systems Applications, DEXA 2020, held in September 2020: The 11th International Workshop on Biological Knowledge Discovery from Data, BIOKDD 2020, the 4th International Workshop on Cyber-Security and Functional Safety in Cyber-Physical Systems, IWCFS 2020, the 2nd International Workshop on Machine Learning and Knowledge Graphs, MLKgraphs2019. Due to the COVID-19 pandemic the conference and workshops were held virtually. The 10 papers were thoroughly reviewed and selected from 15 submissions, and discuss a range of topics including: knowledge discovery, biological data, cyber security, cyber-physical system, machine learning, knowledge graphs, information retriever, data base, and artificial intelligence.