| 2026 | GECCO | EvoBatch: A Mini-Batch, Compute-Constrained Evolutionary Algorithm Reduces the Generalization Gap in Deep Learning. | Toki Tahmid Inan, Shahana Shultana, Amarda Shehu |
| 2025 | GECCO | Closing the Optimization and Generalization Gap in Deep Learning with A Multi-Objective Evolutionary Algorithm. | Toki Tahmid Inan, Shahana Shultana, Amarda Shehu |
| 2025 | KDD | An Instructible Chemist-AI Alignment Framework for Generating Quaternary Ammonium Compound Structures. | Bo Pan, Shiva Ghaemi, Amanda J. Consylman, Zihao Zhao, Ashley Ann Petersen, Alice Wu, Gabriel Chang, Diana McDonough, Mark A. Forman, Elise L. Bezold, William M. Wuest, Kevin Minbiole, Liang Zhao, Amarda Shehu |
| 2025 | SDM | Better AI For Understanding Life on Earth: Predict First, Design Later. | Yana Bromberg, Amarda Shehu |
| 2024 | EMNLP | Birdie: Advancing State Space Language Modeling with Dynamic Mixtures of Training Objectives. | Sam Blouir, Jimmy T. H. Smith, Antonios Anastasopoulos, Amarda Shehu |
| 2024 | GECCO | Revisiting Evolutionary Algorithms for Optimization for Deep Learning: Introducing DL-HEA: EAs for Optimization for Deep Learning. | Toki Tahmid Inan, Amarda Shehu |
| 2022 | ICANN | F-Measure Optimization for Multi-class, Imbalanced Emotion Classification Tasks. | Toki Tahmid Inan, Mingrui Liu, Amarda Shehu |
| 2022 | SDM | Interpretable Molecular Graph Generation via Monotonic Constraints. | Yuanqi Du, Xiaojie Guo, Amarda Shehu, Liang Zhao |
| 2021 | ICANN | Detecting Scarce Emotions Using BERT and Hyperparameter Optimization. | Zahra Rajabi, zlem Uzuner, Amarda Shehu |
| 2020 | KDD | Interpretable Deep Graph Generation with Node-edge Co-disentanglement. | Xiaojie Guo, Liang Zhao, Zhao Qin, Lingfei Wu, Amarda Shehu, Yanfang Ye |
| 2020 | KDD | Reconstruction and Decomposition of High-Dimensional Landscapes via Unsupervised Learning. | Jing Lei, Nasrin Akhter, Wanli Qiao, Amarda Shehu |
| 2019 | GECCO | Using subpopulation EAs to map molecular structure landscapes. | Ahmed Bin Zaman, Kenneth A. De Jong, Amarda Shehu |
| 2017 | CIBCB | Modeling protein structural transitions as a multiobjective optimization problem. | Emmanuel Sapin, Kenneth A. De Jong, Amarda Shehu |
| 2017 | GECCO | Evolutionary search for paths on protein energy landscapes. | Emmanuel Sapin, Kenneth A. De Jong, Amarda Shehu |
| 2017 | GECCO | An evolutionary algorithm to model structural excursions of a protein. | Emmanuel Sapin, Kenneth A. De Jong, Amarda Shehu |
| 2016 | GECCO | Women@GECCO 2016 Chairs' Welcome. | Carola Doerr, Julia Handl, Emma Hart, Gabriela Ochoa, Amarda Shehu, Tea Tusar, Anya E. Vostinar, Christine Zarges, Nur Zincir-Heywood |
| 2016 | GECCO | Workshop Evolutionary Computation in Computational Structural Biology 2016 Chairs' Welcome. | Jos Santos Reyes, Julia Handl, Amarda Shehu |
| 2016 | GECCO | A Novel EA-based Memetic Approach for Efficiently Mapping Complex Fitness Landscapes. | Emmanuel Sapin, Kenneth A. De Jong, Amarda Shehu |
| 2016 | GECCO | Path-based Guidance of an Evolutionary Algorithm in Mapping a Fitness Landscape and its Connectivity. | Emmanuel Sapin, Kenneth A. De Jong, Amarda Shehu |
| 2015 | GECCO | Evolution Strategies for Exploring Protein Energy Landscapes. | Rudy Clausen, Emmanuel Sapin, Kenneth A. De Jong, Amarda Shehu |
| 2015 | GECCO | Mapping Multiple Minima in Protein Energy Landscapes with Evolutionary Algorithms. | Emmanuel Sapin, Kenneth A. De Jong, Amarda Shehu |
| 2015 | GECCO | Evolutionary Algorithms for Protein Structure Modeling. | Amarda Shehu, Kenneth A. De Jong |
| 2014 | GECCO | Evolutionary search algorithms for protein modeling: from de novo structure prediction to comprehensive maps of functionally-relevant structures of protein chains and assemblies. | Amarda Shehu, Kenneth A. De Jong |
| 2013 | GECCO | Off-lattice protein structure prediction with homologous crossover. | Brian S. Olson, Kenneth A. De Jong, Amarda Shehu |
| 2012 | PPSN | A Spatial EA Framework for Parallelizing Machine Learning Methods. | Uday Kamath, Johan Kaers, Amarda Shehu, Kenneth A. De Jong |
| 2011 | CEC | An evolutionary-based approach for feature generation: Eukaryotic promoter recognition. | Uday Kamath, Kenneth A. De Jong, Amarda Shehu |
| 2010 | CEC | Using evolutionary computation to improve SVM classification. | Uday Kamath, Amarda Shehu, Kenneth A. De Jong |
| 2010 | GECCO | Selecting predictive features for recognition of hypersensitive sites of regulatory genomic sequences with an evolutionary algorithm. | Uday Kamath, Kenneth A. De Jong, Amarda Shehu |
| 2009 | PPAM | Automated Design of Assemblable, Modular, Synthetic Chromosomes. | Sarah M. Richardson, Brian S. Olson, Jessica S. Dymond, Randal C. Burns, Srinivasan Chandrasegaran, Jef D. Boeke, Amarda Shehu, Joel S. Bader |