Amarda Shehu - RankMe

171 papers A* 5A 7B 2C 1Journal 62Unranked 90

Year	Rank	Type	Title / Venue / Authors
2026	J	`jnl`	Beyond the Singularity Myth: Artificial General Intelligence as Cumulative Infrastructural Transformation - Absorption Capacity, Epistemic Drift, and the Erosion of Human Verification Power. ACM Trans. Intell. Syst. Technol. Amarda Shehu
2026	J	`jnl`	Can Consumer Chatbots Reason? A Student-Led Field Experiment Embedded in an "AI-for-All" Undergraduate Course. CoRR Amarda Shehu, Adonyas Ababu, Asma Akbary, Griffin Allen, Aroush Baig, Tereana Battle, Elias Beall, Christopher Byrom, Matt Dean, Kate Demarco, Ethan Douglass, Luis Granados, Layla Hantush, Andy Hay, Eleanor Hay, Caleb Jackson, Jaewon Jang, Carter Jones, Quanyang Li, Adrian Lopez, Logan Massimo, Garrett McMullin, Ariana Mendoza Maldonado, Eman Mirza, Hadiya Muddasar, Sara Nuwayhid, Brandon Pak, Ashley Petty, Dryden Rancourt, Lily Rodriguez, Corbin Rogers, Jacob Schiek, Taeseo Seok, Aarav Sethi, Giovanni Vitela, Winston Williams, Jagan Yetukuri
2026	J	`jnl`	Topology-Aware Generation and Activity-Based Filtering: A Computational-Experimental Framework for Data-Scarce Quaternary Ammonium Compound Discovery. J. Chem. Inf. Model. Shiva Ghaemi, Amanda J. Consylman, Bo Pan, Alice Wu, Ashley Ann Petersen, Gabe Chang, Diana McDonough, Mark A. Forman, Elise L. Bezold, William M. Wuest, Amarda Shehu, Liang Zhao, Kevin Minbiole
2025	—	`conf`	An Instructible Chemist-AI Alignment Framework for Generating Quaternary Ammonium Compound Structures. KDD (2) 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	A	`conf`	Better AI For Understanding Life on Earth: Predict First, Design Later. SDM Yana Bromberg, Amarda Shehu
2025	—	`conf`	Closing the Optimization and Generalization Gap in Deep Learning with A Multi-Objective Evolutionary Algorithm. GECCO Companion Toki Tahmid Inan, Shahana Shultana, Amarda Shehu
2025	—	`conf`	DyVarMap: An Interpretable, Dynamics-Aware Framework for Missense Variant Classification. BCB Companion Yiyang Lian, Amarda Shehu
2025	J	`jnl`	Foundation Models for AI-Enabled Biological Design. CoRR Asher Moldwin, Amarda Shehu
2025	—	`conf`	From Contrast to Control: Domain Conditioned Masking for Small Molecule Generation of Quaternary Ammonium Compounds. BCB Companion Shiva Ghaemi, Rehenuma Tasmin Rodoshi, Shahana Shultana, Amarda Shehu, Daniel Barbará
2025	J	`jnl`	The ethics of national artificial intelligence plans: an empirical lens. AI Ethics Manpriya Dua, J. P. Singh, Amarda Shehu
2024	J	`jnl`	Accounting for Work Zone Disruptions in Traffic Flow Forecasting. CoRR Yuanjie Lu, Amarda Shehu, David Lattanzi
2024	J	`jnl`	Beyond Single-Model Views for Deep Learning: Optimization versus Generalizability of Stochastic Optimization Algorithms. CoRR Toki Tahmid Inan, Mingrui Liu, Amarda Shehu
2024	A*	`conf`	Birdie: Advancing State Space Language Modeling with Dynamic Mixtures of Training Objectives. EMNLP Sam Blouir, Jimmy T. H. Smith, Antonios Anastasopoulos, Amarda Shehu
2024	J	`jnl`	Birdie: Advancing State Space Models with Reward-Driven Objectives and Curricula. CoRR Sam Blouir, Jimmy T. H. Smith, Antonios Anastasopoulos, Amarda Shehu
2024	—	`conf`	Revisiting Evolutionary Algorithms for Optimization for Deep Learning: Introducing DL-HEA: EAs for Optimization for Deep Learning. GECCO Companion Toki Tahmid Inan, Amarda Shehu
2023	—	`conf`	A Comparative Analysis of Transformer-based Protein Language Models for Remote Homology Prediction. BCB Anowarul Kabir, Asher Moldwin, Amarda Shehu
2023	J	`jnl`	Adaptive Stochastic Optimization to Improve Protein Conformation Sampling. IEEE ACM Trans. Comput. Biol. Bioinform. Ahmed Bin Zaman, Toki Tahmid Inan, Kenneth A. De Jong, Amarda Shehu
2023	J	`jnl`	Examining DNA breathing with pyDNA-EPBD. Bioinform. Anowarul Kabir, Manish Bhattarai, Kim Ø. Rasmussen, Amarda Shehu, Anny Usheva, Alan R. Bishop, Boian S. Alexandrov
2023	A*	`conf`	Global Convergence Analysis of Local SGD for Two-layer Neural Network without Overparameterization. NeurIPS Yajie Bao, Amarda Shehu, Mingrui Liu
2023	—	`conf`	Structure- and Energy-based Analysis of Small Molecule Ligand Binding to Steroid Nuclear Receptors. BCB Megan Herceg, Amarda Shehu
2022	—	`conf`	Equivariant Encoding based GVAE (EqEn-GVAE) for Protein Tertiary Structure Generation. BIBM Taseef Rahman, Fardina Fathmiul Alam, Amarda Shehu
2022	—	`conf`	F-Measure Optimization for Multi-class, Imbalanced Emotion Classification Tasks. ICANN (1) Toki Tahmid Inan, Mingrui Liu, Amarda Shehu
2022	—	`conf`	Generation and Characterization of Quaternary Ammonium Compounds via Deep Learning. BIBM Yinkai Wang, Shiva Ghaemi, Aowei Ding, Yuanqui Du, Bo Pan, Muran Qin, Xuanyang Lin, Ashley Ann Petersen, Austin Leitgeb, Saleh AlKhalifa, Kevin Minbiole, William M. Wuest, Liang Zhao, Amarda Shehu
2022	J	`jnl`	Improved Protein Decoy Selection via Non-Negative Matrix Factorization. IEEE ACM Trans. Comput. Biol. Bioinform. Nasrin Akhter, Kazi Lutful Kabir, Gopinath Chennupati, Raviteja Vangara, Boian S. Alexandrov, Hristo N. Djidjev, Amarda Shehu
2022	A	`conf`	Interpretable Molecular Graph Generation via Monotonic Constraints. SDM Yuanqi Du, Xiaojie Guo, Amarda Shehu, Liang Zhao
2022	J	`jnl`	Interpretable Molecular Graph Generation via Monotonic Constraints. CoRR Yuanqi Du, Xiaojie Guo, Amarda Shehu, Liang Zhao
2022	A*	`conf`	Multi-objective Deep Data Generation with Correlated Property Control. NeurIPS Shiyu Wang, Xiaojie Guo, Xuanyang Lin, Bo Pan, Yuanqi Du, Yinkai Wang, Yanfang Ye, Ashley Ann Petersen, Austin Leitgeb, Saleh AlKhalifa, Kevin Minbiole, William M. Wuest, Amarda Shehu, Liang Zhao
2022	J	`jnl`	Multi-objective Deep Data Generation with Correlated Property Control. CoRR Shiyu Wang, Xiaojie Guo, Xuanyang Lin, Bo Pan, Yuanqi Du, Yinkai Wang, Yanfang Ye, Ashley Ann Petersen, Austin Leitgeb, Saleh AlKhalifa, Kevin Minbiole, William M. Wuest, Amarda Shehu, Liang Zhao
2022	J	`jnl`	Multiple Instance Learning for Detecting Anomalies over Sequential Real-World Datasets. CoRR Parastoo Kamranfar, David Lattanzi, Amarda Shehu, Daniel Barbará
2022	J	`jnl`	Pavement Distress Recognition via Wavelet-Based Clustering of Smartphone Accelerometer Data. J. Comput. Civ. Eng. Parastoo Kamranfar, David Lattanzi, Amarda Shehu, Shelley Stoffels
2022	—	`conf`	Property-Controllable Generation of Quaternary Ammonium Compounds. BIBM Bo Pan, Yinkai Wang, Xuanyang Lin, Muran Qin, Yuanqi Du, Shiva Ghaemi, Aowei Ding, Shiyu Wang, Saleh AlKhalifa, Kevin Minbiole, William M. Wuest, Ashley Ann Petersen, Austin Leitgeb, Amarda Shehu, Liang Zhao
2022	—	`conf`	Sequence-Structure Embeddings via Protein Language Models Improve on Prediction Tasks. ICKG Anowarul Kabir, Amarda Shehu
2022	J	`jnl`	Small molecule generation via disentangled representation learning. Bioinform. Yuanqi Du, Xiaojie Guo, Yinkai Wang, Amarda Shehu, Liang Zhao
2022	J	`jnl`	Transformer Neural Networks Attending to Both Sequence and Structure for Protein Prediction Tasks. CoRR Anowarul Kabir, Amarda Shehu
2021	—	`conf`	Antigen Binding Reshapes Antibody Energy Landscape and Conformation Dynamics. BIBM Kazi Lutful Kabir, Ruth Nussinov, Buyong Ma, Amarda Shehu
2021	—	`conf`	Deep Latent-Variable Models for Controllable Molecule Generation. BIBM Yuanqi Du, Yinkai Wang, Fardina Fathmiul Alam, Yuanjie Lu, Xiaojie Guo, Liang Zhao, Amarda Shehu
2021	—	`conf`	Detecting Scarce Emotions Using BERT and Hyperparameter Optimization. ICANN (5) Zahra Rajabi, Özlem Uzuner, Amarda Shehu
2021	—	`conf`	Generating Physically-Realistic Tertiary Protein Structures with Deep Latent Variable Models Learning Over Experimentally-available Structures. BIBM Fardina Fathmiul Alam, Amarda Shehu
2021	—	`conf`	Graph Representation Learning for Protein Conformation Sampling. ICCABS Taseef Rahman, Yuanqi Du, Amarda Shehu
2021	—	`conf`	PsychBERT: A Mental Health Language Model for Social Media Mental Health Behavioral Analysis. BIBM Vedant Vajre, Mitchell Naylor, Uday Kamath, Amarda Shehu
2021	—	`conf`	Single Model Quality Estimation of Protein Structures via Non-negative Tensor Factorization. ICCABS Kazi Lutful Kabir, Manish Bhattarai, Boian S. Alexandrov, Amarda Shehu
2021	J	`jnl`	Space Partitioning and Regression Mode Seeking via a Mean-Shift-Inspired Algorithm. CoRR Wanli Qiao, Amarda Shehu
2021	J	`jnl`	Traffic Flow Forecasting with Maintenance Downtime via Multi-Channel Attention-Based Spatio-Temporal Graph Convolutional Networks. CoRR Yuanjie Lu, Parastoo Kamranfar, David Lattanzi, Amarda Shehu
2021	J	`jnl`	Unsupervised multi-instance learning for protein structure determination. J. Bioinform. Comput. Biol. Fardina Fathmiul Alam, Amarda Shehu
2020	—	`conf`	A Multi-channel BiLSTM-CNN Model for Multilabel Emotion Classification of Informal Text. ICSC Zahra Rajabi, Amarda Shehu, Özlem Uzuner
2020	J	`jnl`	Decoy Selection for Protein Structure Prediction Via Extreme Gradient Boosting and Ranking. CoRR Nasrin Akhter, Gopinath Chennupati, Hristo N. Djidjev, Amarda Shehu
2020	—	`conf`	Decoy Selection in Protein Structure Determination via Symmetric Non-negative Matrix Factorization. BIBM Kazi Lutful Kabir, Gopinath Chennupati, Raviteja Vangara, Hristo N. Djidjev, Boian S. Alexandrov, Amarda Shehu
2020	J	`jnl`	Decoy selection for protein structure prediction via extreme gradient boosting and ranking. BMC Bioinform. Nasrin Akhter, Gopinath Chennupati, Hristo N. Djidjev, Amarda Shehu
2020	—	`conf`	Deep Ranking in Template-free Protein Structure Prediction. BCB Xiao Chen, Nasrin Akhter, Zhiye Guo, Tianqi Wu, Jie Hou, Amarda Shehu, Jianlin Cheng
2020	J	`jnl`	Generating Tertiary Protein Structures via an Interpretative Variational Autoencoder. CoRR Xiaojie Guo, Sivani Tadepalli, Liang Zhao, Amarda Shehu
2020	J	`jnl`	Interpretable Deep Graph Generation with Node-Edge Co-Disentanglement. CoRR Xiaojie Guo, Liang Zhao, Zhao Qin, Lingfei Wu, Amarda Shehu, Yanfang Ye
2020	A*	`conf`	Interpretable Deep Graph Generation with Node-edge Co-disentanglement. KDD Xiaojie Guo, Liang Zhao, Zhao Qin, Lingfei Wu, Amarda Shehu, Yanfang Ye
2020	—	`conf`	Protein Decoy Generation via Adaptive Stochastic Optimization for Protein Structure Determination. BIBM Ahmed Bin Zaman, Toki Tahmid Inan, Amarda Shehu
2020	A*	`conf`	Reconstruction and Decomposition of High-Dimensional Landscapes via Unsupervised Learning. KDD Jing Lei, Nasrin Akhter, Wanli Qiao, Amarda Shehu
2020	—	`conf`	Variational Autoencoders for Protein Structure Prediction. BCB Fardina Fathmiul Alam, Amarda Shehu
2019	J	`jnl`	Attenuating dependence on structural data in computing protein energy landscapes. BMC Bioinform. David Morris, Tatiana Maximova, Erion Plaku, Amarda Shehu
2019	J	`jnl`	Balancing multiple objectives in conformation sampling to control decoy diversity in template-free protein structure prediction. BMC Bioinform. Ahmed Bin Zaman, Amarda Shehu
2019	J	`jnl`	Building maps of protein structure spaces in template-free protein structure prediction. J. Bioinform. Comput. Biol. Ahmed Bin Zaman, Amarda Shehu
2019	—	`conf`	Decoy Ensemble Reduction in Template-free Protein Structure Prediction. BCB Ahmed Bin Zaman, Parastoo Kamranfar, Carlotta Domeniconi, Amarda Shehu
2019	—	`ch.`	EML: A Scalable, Transparent Meta-Learning Paradigm for Big Data Applications. Innovations in Big Data Mining and Embedded Knowledge Uday Kamath, Carlotta Domeniconi, Amarda Shehu, Kenneth A. De Jong
2019	J	`jnl`	From molecular energy landscapes to equilibrium dynamics via landscape analysis and markov state models. J. Bioinform. Comput. Biol. Kazi Lutful Kabir, Nasrin Akhter, Amarda Shehu
2019	J	`jnl`	Guest Editorial for the ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics. IEEE ACM Trans. Comput. Biol. Bioinform. Amarda Shehu, Giuseppe Pozzi, Tamer Kahveci
2019	J	`jnl`	Guest Editorial on the Special Issue on Informatics on Biomedical Data Learning, Reasoning, and Representation. IEEE J. Biomed. Health Informatics Tamer Kahveci, Giuseppe Pozzi, Amarda Shehu, May Dongmei Wang
2019	—	`conf`	Identifying Near-Native Protein Structures via Anomaly Detection. BIBM Sivani Tadepalli, Nasrin Akhter, Daniel Barbará, Amarda Shehu
2019	—	`conf`	Learning Reduced Latent Representations of Protein Structure Data. BCB Fardina Fathmiul Alam, Taseef Rahman, Amarda Shehu
2019	—	`conf`	Non-Negative Matrix Factorization for Selection of Near-Native Protein Tertiary Structures. BIBM Nasrin Akhter, Raviteja Vangara, Gopinath Chennupati, Boian S. Alexandrov, Hristo N. Djidjev, Amarda Shehu
2019	J	`jnl`	ROMEO: A Plug-and-play Software Platform of Robotics-inspired Algorithms for Modeling Biomolecular Structures and Motions. CoRR Kevin Molloy, Erion Plaku, Amarda Shehu
2019	—	`conf`	User Behavior Modelling for Fake Information Mitigation on Social Web. SBP-BRiMS Zahra Rajabi, Amarda Shehu, Hemant Purohit
2019	—	`conf`	Using Sequence-Predicted Contacts to Guide Template-free Protein Structure Prediction. BCB Ahmed Bin Zaman, Prasanna Venkatesh Parthasarathy, Amarda Shehu
2019	A	`conf`	Using subpopulation EAs to map molecular structure landscapes. GECCO Ahmed Bin Zaman, Kenneth A. De Jong, Amarda Shehu
2018	J	`jnl`	Advances in the Application and Development of Non-Linear Global Optimization Techniques in Computational Structural Biology. IEEE ACM Trans. Comput. Biol. Bioinform. Julia Handl, Amarda Shehu, José Santos Reyes
2018	J	`jnl`	An Energy Landscape Treatment of Decoy Selection in Template-Free Protein Structure Prediction. Comput. Nasrin Akhter, Wanli Qiao, Amarda Shehu
2018	—	`conf`	Analysis of Molecular Structure Data]{Systematic Study of Different Design Decisions in Markov Model-based Analysis of Molecular Structure Data: Extended Abstract. BCB Sharmila Roychoudhury, Amarda Shehu
2018	—	`conf`	Community Detection for Decoy Selection in Template-free Protein Structure Prediction. BCB Liban Hassan, Zahra Rajabi, Nasrin Akhter, Amarda Shehu
2018	J	`jnl`	Deep learning improves antimicrobial peptide recognition. Bioinform. Daniel Veltri, Uday Kamath, Amarda Shehu
2018	J	`jnl`	From Optimization to Mapping: An Evolutionary Algorithm for Protein Energy Landscapes. IEEE ACM Trans. Comput. Biol. Bioinform. Emmanuel Sapin, Kenneth A. De Jong, Amarda Shehu
2018	—	`conf`	Guiding Exploration of Antimicrobial Peptide Space with a Deep Neural Network. BIBM Manpriya Dua, Daniel Veltri, Barney Bishop, Amarda Shehu
2018	—	`conf`	Improved Decoy Selection via Machine Learning and Ranking. ICCABS Nasrin Akhter, Gopinath Chennupati, Hristo N. Djidjev, Amarda Shehu
2018	—	`conf`	Modeling Macromolecular Structures and Motions: Computational Methods for Sampling and Analysis of Energy Landscapes. BCB Kevin Molloy, Nasrin Akhter, Amarda Shehu
2018	—	`conf`	Modeling the Tertiary Structure of a Multi-domain Protein: Structure Prediction of Multi-domain Proteins. BCB Fahad Almsned, Gideon K. Gogovi, Nicole Bracci, Kylene Kehn-Hall, Estela Blaisten-Barojas, Amarda Shehu
2018	—	`ed.`	Proceedings of the 2018 ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics, BCB 2018, Washington, DC, USA, August 29 - September 01, 2018 BCB Amarda Shehu, Cathy H. Wu, Christina Boucher, Jing Li, Hongfang Liu, Mihai Pop
2018	—	`conf`	Reconstructing and Decomposing Protein Energy Landscapes to Organize Structure Spaces and Reveal Biologically-active States. BIBM Nasrin Akhter, Jing Lei, Wanli Qiao, Amarda Shehu
2018	J	`jnl`	Sample-Based Models of Protein Energy Landscapes and Slow Structural Rearrangements. J. Comput. Biol. Tatiana Maximova, Zijing Zhang, Daniel Carr, Erion Plaku, Amarda Shehu
2018	J	`jnl`	Structure-Guided Protein Transition Modeling with a Probabilistic Roadmap Algorithm. IEEE ACM Trans. Comput. Biol. Bioinform. Tatiana Maximova, Erion Plaku, Amarda Shehu
2017	—	`conf`	ACM-BCB '17 Tutorial: Robotics-inspired Algorithms for Modeling Protein Structures and Motions. BCB Kevin Molloy, David Morris, Amarda Shehu
2017	—	`conf`	An evolutionary algorithm to model structural excursions of a protein. GECCO (Companion) Emmanuel Sapin, Kenneth A. De Jong, Amarda Shehu
2017	—	`conf`	Evolutionary search for paths on protein energy landscapes. GECCO (Companion) Emmanuel Sapin, Kenneth A. De Jong, Amarda Shehu
2017	—	`conf`	Evolving Conformation Paths to Model Protein Structural Transitions. BCB Emmanuel Sapin, Kenneth A. De Jong, Amarda Shehu
2017	J	`jnl`	Guest Editorial for Special Section on BIBM 2014. IEEE ACM Trans. Comput. Biol. Bioinform. Illhoi Yoo, Amarda Shehu
2017	—	`conf`	Highlights Talks at ACM BCB 2017. BCB Amarda Shehu, Tamer Kahveci, Giuseppe Pozzi
2017	J	`jnl`	Improving Recognition of Antimicrobial Peptides and Target Selectivity through Machine Learning and Genetic Programming. IEEE ACM Trans. Comput. Biol. Bioinform. Daniel Veltri, Uday Kamath, Amarda Shehu
2017	C	`conf`	Modeling protein structural transitions as a multiobjective optimization problem. CIBCB Emmanuel Sapin, Kenneth A. De Jong, Amarda Shehu
2017	—	`conf`	Out of one, many: Exploiting intrinsic motions to explore protein structure spaces. ICCABS David Morris, Tatiana Maximova, Erion Plaku, Amarda Shehu
2017	—	`ed.`	Proceedings of the 8th ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics, BCB 2017, Boston, MA, USA, August 20-23, 2017 BCB Nurit Haspel, Lenore J. Cowen, Amarda Shehu, Tamer Kahveci, Giuseppe Pozzi
2017	—	`conf`	Reconstructing and mining protein energy landscape to understand disease. BIBM Wanli Qiao, Tatiana Maximova, Xiaowen Fang, Erion Plaku, Amarda Shehu
2017	—	`conf`	Statistical Analysis of Computed Energy Landscapes to Understand Dysfunction in Pathogenic Protein Variants. BCB Wanli Qiao, Tatiana Maximova, Erion Plaku, Amarda Shehu
2017	—	`conf`	The 2017 Computational Structural Bioinformatics Workshop: CSBW 2017. BCB Nurit Haspel, Amarda Shehu, Kevin Molloy
2016	A	`conf`	A Novel EA-based Memetic Approach for Efficiently Mapping Complex Fitness Landscapes. GECCO Emmanuel Sapin, Kenneth A. De Jong, Amarda Shehu
2016	J	`jnl`	A Survey of Computational Treatments of Biomolecules by Robotics-Inspired Methods Modeling Equilibrium Structure and Dynamic. J. Artif. Intell. Res. Amarda Shehu, Erion Plaku
2016	J	`jnl`	A stochastic roadmap method to model protein structural transitions. Robotica Kevin Molloy, Rudy Clausen, Amarda Shehu
2016	J	`jnl`	Foreword on special issue on robotics methods for structural and dynamic modeling of molecular systems. Robotica Lydia Tapia, Juan Cortés, Amarda Shehu, Jinalin Chen
2016	—	`conf`	Path-based Guidance of an Evolutionary Algorithm in Mapping a Fitness Landscape and its Connectivity. GECCO (Companion) Emmanuel Sapin, Kenneth A. De Jong, Amarda Shehu
2016	J	`jnl`	Principles and Overview of Sampling Methods for Modeling Macromolecular Structure and Dynamics. PLoS Comput. Biol. Tatiana Maximova, Ryan Moffatt, Buyong Ma, Ruth Nussinov, Amarda Shehu
2016	—	`conf`	Sample-based Models of Protein Structural Transitions. BCB Tatiana Maximova, Daniel Carr, Erion Plaku, Amarda Shehu
2016	—	`conf`	Women@GECCO 2016 Chairs' Welcome. GECCO (Companion) Carola Doerr, Julia Handl, Emma Hart, Gabriela Ochoa, Amarda Shehu, Tea Tusar, Anya E. Vostinar, Christine Zarges, Nur Zincir-Heywood
2016	—	`conf`	Workshop Evolutionary Computation in Computational Structural Biology 2016 Chairs' Welcome. GECCO (Companion) José Santos Reyes, Julia Handl, Amarda Shehu
2015	—	`ed.`	2015 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2015, Washington, DC, USA, November 9-12, 2015 BIBM Jun Huan, Satoru Miyano, Amarda Shehu, Xiaohua Tony Hu, Bin Ma, Sanguthevar Rajasekaran, Vijay K. Gombar, Matthieu-P. Schapranow, Illhoi Yoo, Jiayu Zhou, Brian Chen, Vinay Pai, Brian G. Pierce
2015	J	`jnl`	A Data-Driven Evolutionary Algorithm for Mapping Multibasin Protein Energy Landscapes. J. Comput. Biol. Rudy Clausen, Amarda Shehu
2015	J	`jnl`	Computational Methods for Exploration and Analysis of Macromolecular Structure and Dynamics. PLoS Comput. Biol. Amarda Shehu, Ruth Nussinov
2015	—	`conf`	Computing transition paths in multiple-basin proteins with a probabilistic roadmap algorithm guided by structure data. BIBM Tatiana Maximova, Erion Plaku, Amarda Shehu
2015	A	`conf`	Evolution Strategies for Exploring Protein Energy Landscapes. GECCO Rudy Clausen, Emmanuel Sapin, Kenneth A. De Jong, Amarda Shehu
2015	—	`conf`	Evolutionary Algorithms for Protein Structure Modeling. GECCO (Companion) Amarda Shehu, Kenneth A. De Jong
2015	—	`conf`	Evolutionary search strategies for efficient sample-based representations of multiple-basin protein energy landscapes. BIBM Emmanuel Sapin, Kenneth A. De Jong, Amarda Shehu
2015	—	`conf`	Interleaving Global and Local Search for Protein Motion Computation. ISBRA Kevin Molloy, Amarda Shehu
2015	—	`conf`	Mapping Multiple Minima in Protein Energy Landscapes with Evolutionary Algorithms. GECCO (Companion) Emmanuel Sapin, Kenneth A. De Jong, Amarda Shehu
2015	J	`jnl`	Mapping the Conformation Space of Wildtype and Mutant H-Ras with a Memetic, Cellular, and Multiscale Evolutionary Algorithm. PLoS Comput. Biol. Rudy Clausen, Buyong Ma, Ruth Nussinov, Amarda Shehu
2015	J	`jnl`	The 7th Computational Structural Bioinformatics Workshop. J. Comput. Biol. Jing He, Amarda Shehu, Nurit Haspel, Brian Chen
2015	J	`jnl`	idDock+: Integrating Machine Learning in Probabilistic Search for Protein-Protein Docking. J. Comput. Biol. Irina Hashmi, Amarda Shehu
2014	—	`conf`	A multiscale hybrid evolutionary algorithm to obtain sample-based representations of multi-basin protein energy landscapes. BCB Rudy Clausen, Amarda Shehu
2014	—	`conf`	A novel method to improve recognition of antimicrobial peptides through distal sequence-based features. BIBM Daniel Veltri, Uday Kamath, Amarda Shehu
2014	—	`conf`	Evolutionary search algorithms for protein modeling: from de novo structure prediction to comprehensive maps of functionally-relevant structures of protein chains and assemblies. GECCO (Companion) Amarda Shehu, Kenneth A. De Jong
2014	J	`jnl`	Exploring representations of protein structure for automated remote homology detection and mapping of protein structure space. BMC Bioinform. Kevin Molloy, M. Jennifer Van, Daniel Barbará, Amarda Shehu
2014	—	`conf`	Knowledge-based search and multi-objective filters: proposed structural models of GPCR dimerization. BCB Irina Hashmi, Daniel Veltri, Nadine Kabbani, Amarda Shehu
2014	—	`conf`	Sampling-based methods for a full characterization of energy landscapes of small peptides. BIBM Didier Devaurs, Amarda Shehu, Thierry Siméon, Juan Cortés
2013	—	`conf`	A PCA-guided Search Algorithm to Probe the Conformational Space of the Ras Protein. BCB Rudy Clausen, Amarda Shehu
2013	—	`conf`	Binary Response Models for Recognition of Antimicrobial Peptides. BCB Elena G. Randou, Daniel Veltri, Amarda Shehu
2013	—	`conf`	Exploring the Structure Space of Wildtype Ras Guided by Experimental Data. BCB Rudy Clausen, Amarda Shehu
2013	—	`conf`	Higher-order representations of protein structure space. ICCABS Kevin Molloy, M. Jennifer Van, Daniel Barbará, Amarda Shehu
2013	—	`conf`	Informatics-driven Protein-protein Docking. BCB Irina Hashmi, Amarda Shehu
2013	—	`conf`	Multi-Objective Stochastic Search for Sampling Local Minima in the Protein Energy Surface. BCB Brian S. Olson, Amarda Shehu
2013	A	`conf`	Off-lattice protein structure prediction with homologous crossover. GECCO Brian S. Olson, Kenneth A. De Jong, Amarda Shehu
2013	J	`jnl`	Probabilistic Search and Energy Guidance for Biased Decoy Sampling in Ab Initio Protein Structure Prediction. IEEE ACM Trans. Comput. Biol. Bioinform. Kevin Molloy, Sameh N. Saleh, Amarda Shehu
2013	—	`conf`	Protein-protein Docking Using Information from Native Interaction Interfaces. BCB Irina Hashmi, Amarda Shehu
2013	—	`conf`	Systematic analysis of global features and model building for recognition of antimicrobial peptides. ICCABS Elena G. Randou, Daniel Veltri, Amarda Shehu
2013	J	`jnl`	The AAAI-13 Conference Workshops. AI Mag. Vikas Agrawal, Christopher Archibald, Mehul Bhatt, Hung Bui, Diane J. Cook, Juan Cortés, Christopher W. Geib, Vibhav Gogate, Hans W. Guesgen, Dietmar Jannach, Michael Johanson, Kristian Kersting, George Dimitri Konidaris, Lars Kotthoff, Martin Michalowski, Sriraam Natarajan, Barry O'Sullivan, Marc Pickett, Vedran Podobnik, David Poole, Lokendra Shastri, Amarda Shehu, Gita Sukthankar
2012	—	`conf`	A Spatial EA Framework for Parallelizing Machine Learning Methods. PPSN (1) Uday Kamath, Johan Kaers, Amarda Shehu, Kenneth A. De Jong
2012	—	`conf`	A basin hopping algorithm for protein-protein docking. BIBM Irina Hashmi, Amarda Shehu
2012	—	`conf`	A population-based evolutionary algorithm for sampling minima in the protein energy surface. BIBM Workshops Sameh N. Saleh, Brian S. Olson, Amarda Shehu
2012	—	`conf`	A robotics-inspired method to sample conformational paths connecting known functionally-relevant structures in protein systems. BIBM Workshops Kevin Molloy, Amarda Shehu
2012	—	`conf`	A tree-based search to bias sampling of protein decoy conformations. BIBM Workshops Kevin Molloy, Amarda Shehu
2012	J	`jnl`	An Evolutionary Algorithm Approach for Feature Generation from Sequence Data and Its Application to DNA Splice Site Prediction. IEEE ACM Trans. Comput. Biol. Bioinform. Uday Kamath, Jack Compton, Rezarta Islamaj Dogan, Kenneth A. De Jong, Amarda Shehu
2012	J	`jnl`	An Evolutionary conservation-Based Method for Refining and Reranking protein Complex Structures. J. Bioinform. Comput. Biol. Bahar Akbal-Delibas, Irina Hashmi, Amarda Shehu, Nurit Haspel
2012	—	`conf`	An evolutionary framework to sample near-native protein conformations. BIBM Workshops Sameh N. Saleh, Brian S. Olson, Amarda Shehu
2012	—	`conf`	An evolutionary search framework to efficiently sample local minima in the protein conformational space. BCB Brian S. Olson, Amarda Shehu
2012	J	`jnl`	Basin Hopping as a General and Versatile Optimization Framework for the Characterization of Biological Macromolecules. Adv. Artif. Intell. Brian S. Olson, Irina Hashmi, Kevin Molloy, Amarda Shehu
2012	—	`conf`	Biased decoy sampling to aid the selection of near-native protein conformations. BCB Kevin Molloy, Amarda Shehu
2012	—	`conf`	Efficient basin hopping in the protein energy surface. BIBM Brian S. Olson, Amarda Shehu
2012	J	`jnl`	Guiding Probabilistic Search of the protein conformational Space with Structural Profiles. J. Bioinform. Comput. Biol. Brian S. Olson, Kevin Molloy, S. Farid Hendi, Amarda Shehu
2012	J	`jnl`	Guiding protein docking with Geometric and Evolutionary Information. J. Bioinform. Comput. Biol. Irina Hashmi, Bahar Akbal-Delibas, Nurit Haspel, Amarda Shehu
2012	—	`conf`	Jumping low, jumping high: Controlling hopping in the protein energy surface. BIBM Workshops Brian S. Olson, Amarda Shehu
2012	—	`conf`	Mapping conformational pathways between known functional protein states. BIBM Workshops Kevin Molloy, Amarda Shehu
2012	J	`jnl`	Modeling Structures and Motions of Loops in Protein Molecules. Entropy Amarda Shehu, Lydia E. Kavraki
2012	—	`conf`	Physico-chemical features for recognition of antimicrobial peptides. BIBM Workshops Daniel Veltri, Amarda Shehu
2012	—	`conf`	Sampling low-energy protein-protein configurations with basin hopping. BIBM Workshops Irina Hashmi, Amarda Shehu
2011	J	`jnl`	A Two-Stage Evolutionary Approach for Effective Classification of hypersensitive DNA Sequences. J. Bioinform. Comput. Biol. Uday Kamath, Amarda Shehu, Kenneth A. De Jong
2011	B	`conf`	An evolutionary-based approach for feature generation: Eukaryotic promoter recognition. IEEE Congress on Evolutionary Computation Uday Kamath, Kenneth A. De Jong, Amarda Shehu
2011	—	`conf`	Assembly of low-energy protein conformations with heterogeneous fragments. BIBM Workshops Kevin Molloy, Amarda Shehu
2011	J	`jnl`	In Search of the protein Native State with a Probabilistic Sampling Approach. J. Bioinform. Comput. Biol. Brian S. Olson, Kevin Molloy, Amarda Shehu
2011	—	`conf`	Populating Local Minima in the Protein Conformational Space. BIBM Brian S. Olson, Amarda Shehu
2011	—	`conf`	Protein conformational search with geometric projections. BIBM Workshops Brian S. Olson, S. Farid Hendi, Amarda Shehu
2011	—	`conf`	Protein docking with information on evolutionary conserved interfaces. BIBM Workshops Irina Hashmi, Bahar Akbal-Delibas, Nurit Haspel, Amarda Shehu
2011	—	`conf`	Refinement of docked protein complex structures using evolutionary traces. BIBM Workshops Bahar Akbal-Delibas, Irina Hashmi, Amarda Shehu, Nurit Haspel
2011	J	`jnl`	The 5th International Conference on Bio-Inspired Models of Network, Information and Computing Systems (Bionetics 2010) Special Track on Bioinformatics. J. Bioinform. Comput. Biol. Nurit Haspel, Amarda Shehu
2010	—	`conf`	Enhancing Sampling of the Conformational Space Near the Protein Native State. BIONETICS Brian S. Olson, Kevin Molloy, Amarda Shehu
2010	—	`conf`	Feature and Kernel Evolution for Recognition of Hypersensitive Sites in DNA Sequences. BIONETICS Uday Kamath, Amarda Shehu, Kenneth A. De Jong
2010	J	`jnl`	Guiding the Search for Native-like Protein Conformations with an Ab-initio Tree-based Exploration. Int. J. Robotics Res. Amarda Shehu, Brian S. Olson
2010	A	`conf`	Selecting predictive features for recognition of hypersensitive sites of regulatory genomic sequences with an evolutionary algorithm. GECCO Uday Kamath, Kenneth A. De Jong, Amarda Shehu
2010	B	`conf`	Using evolutionary computation to improve SVM classification. IEEE Congress on Evolutionary Computation Uday Kamath, Amarda Shehu, Kenneth A. De Jong
2009	—	`conf`	An Ab-initio tree-based exploration to enhance sampling of low-energy protein conformations. Robotics: Science and Systems Amarda Shehu
2009	—	`conf`	Automated Design of Assemblable, Modular, Synthetic Chromosomes. PPAM (2) Sarah M. Richardson, Brian S. Olson, Jessica S. Dymond, Randal C. Burns, Srinivasan Chandrasegaran, Jef D. Boeke, Amarda Shehu, Joel S. Bader
2007	J	`jnl`	Sampling Conformation Space to Model Equilibrium Fluctuations in Proteins. Algorithmica Amarda Shehu, Cecilia Clementi, Lydia E. Kavraki