| 2025 | GECCO | Ant Colony Optimization with Policy Gradients and Replay. | William Jardee, John Sheppard |
| 2022 | CEC | Multi-Objective Factored Evolutionary Optimization and the Multi-Objective Knapsack Problem. | Amy Peerlinck, John Sheppard |
| 2022 | ICMLA | Approximate Orthogonal Spectral Autoencoders for Community Analysis in Social Networks. | Scott Wahl, John Sheppard |
| 2022 | IJCNN | Robust Spectral Based Compression of Hyperspectral Images using LSTM Autoencoders. | Kyle Webster, John Sheppard |
| 2021 | IJCNN | Hyperspectral Band Selection for Multispectral Image Classification with Convolutional Networks. | Giorgio Morales, John Sheppard, Riley D. Logan, Joseph A. Shaw |
| 2019 | CEC | Optimal Design of Experiments for Precision Agriculture Using a Genetic Algorithm. | Amy Peerlinck, John Sheppard, Julie Pastorino, Bruce D. Maxwell |
| 2019 | FlAIRS | Spatially Biased Random Forests. | Benjamin Mitchell, John Sheppard |
| 2019 | ICMLA | Legislative Vote Prediction using Campaign Donations and Fuzzy Hierarchical Communities. | Scott Wahl, John Sheppard, Elizabeth Shanahan |
| 2019 | IJCNN | Exploring Transferability in Deep Neural Networks with Functional Data Analysis and Spatial Statistics. | Richard McAllister, John Sheppard |
| 2019 | IJCNN | AdaBoost with Neural Networks for Yield and Protein Prediction in Precision Agriculture. | Amy Peerlinck, John Sheppard, Jacob J. Senecal |
| 2018 | FlAIRS | Evaluating Spatial Generalization of Stacked Autoencoders in Wind Vector Determination. | Richard McAllister, John Sheppard |
| 2018 | TrustCom | Cloud Investigations of Illegal IPTV Networks. | John Sheppard |
| 2017 | FlAIRS | Fuzzy Spectral Hierarchical Communities in Evolving Political Contribution Networks. | Scott Wahl, John Sheppard |
| 2015 | FlAIRS | Hierarchical Fuzzy Spectral Clustering in Social Networks using Spectral Characterization. | Scott Wahl, John Sheppard |
| 2012 | ICMLA | Taxonomic Dimensionality Reduction in Bayesian Text Classification. | Richard McAllister, John Sheppard |
| 2005 | WEBIST | The Use of Data Mining in the Implementation of a Network Intrusion Detection System. | John Sheppard, Joe Carthy, John Dunnion |
| 2003 | ICCSA | Textual CBR for Incident Report Retrieval. | David C. Wilson, Joe Carthy, Karl Abbey, John Sheppard, Ruichao Wang, John Dunnion, Anne Drummond |
| 1999 | CEC | Genetic programming and co-evolution with exogenous fitness in an artificial life environment. | Michael Waters, John Sheppard |