| 2019 | AAAI | Probabilistic-Logic Bots for Efficient Evaluation of Business Rules Using Conversational Interfaces. | Joseph Bockhorst, Devin Conathan, Glenn Moo Fung |
| 2018 | ICMLA | Using Discriminative Graphical Models for Insurance Recommender Systems. | Teja Kanchinadam, Maleeha Qazi, Joseph Bockhorst, Mary Y. Morell, Katie J. Meissner, Glenn Fung |
| 2007 | ISMB | Connecting quantitative regulatory-network models to the genome. | Yue Pan, Tim Durfee, Joseph Bockhorst, Mark Craven |
| 2007 | UAI | Discovering Patterns in Biological Sequences by Optimal Segmentation. | Joseph Bockhorst, Nebojsa Jojic |
| 2004 | ILP | FOIL-D: Efficiently Scaling FOIL for Multi-relational Data Mining of Large Datasets. | Joseph Bockhorst, Irene M. Ong |
| 2003 | ISMB | Predicting bacterial transcription units using sequence and expression data. | Joseph Bockhorst, Yu Qiu, Jeremy D. Glasner, Mingzhu Liu, Frederick R. Blattner, Mark Craven |
| 2002 | ICML | Exploiting Relations Among Concepts to Acquire Weakly Labeled Training Data. | Joseph Bockhorst, Mark Craven |
| 2001 | IJCAI | Refining the Structure of a Stochastic Context-Free Grammar. | Joseph Bockhorst, Mark Craven |
| 2000 | ICML | Using Multiple Levels of Learning and Diverse Evidence to Uncover Coordinately Controlled Genes. | Mark W. Craven, David Page, Jude W. Shavlik, Joseph Bockhorst, Jeremy D. Glasner |
| 2000 | ISMB | A Probabilistic Learning Approach to Whole-Genome Operon Prediction. | Mark W. Craven, David Page, Jude W. Shavlik, Joseph Bockhorst, Jeremy D. Glasner |