Amarda Shehu
Orcid: 0000-0001-5230-4610Affiliations:
- George Mason University, Fairfax VA, USA
According to our database1,
Amarda Shehu
authored at least 155 papers
between 2007 and 2024.
Collaborative distances:
Collaborative distances:
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Online presence:
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on zbmath.org
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on orkg.org
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on orcid.org
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on cs.gmu.edu
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on dl.acm.org
On csauthors.net:
Bibliography
2024
Beyond Single-Model Views for Deep Learning: Optimization versus Generalizability of Stochastic Optimization Algorithms.
CoRR, 2024
2023
IEEE ACM Trans. Comput. Biol. Bioinform., 2023
Global Convergence Analysis of Local SGD for Two-layer Neural Network without Overparameterization.
Proceedings of the Advances in Neural Information Processing Systems 36: Annual Conference on Neural Information Processing Systems 2023, 2023
A Comparative Analysis of Transformer-based Protein Language Models for Remote Homology Prediction.
Proceedings of the 14th ACM International Conference on Bioinformatics, 2023
Structure- and Energy-based Analysis of Small Molecule Ligand Binding to Steroid Nuclear Receptors.
Proceedings of the 14th ACM International Conference on Bioinformatics, 2023
2022
IEEE ACM Trans. Comput. Biol. Bioinform., 2022
Pavement Distress Recognition via Wavelet-Based Clustering of Smartphone Accelerometer Data.
J. Comput. Civ. Eng., 2022
Multiple Instance Learning for Detecting Anomalies over Sequential Real-World Datasets.
CoRR, 2022
Transformer Neural Networks Attending to Both Sequence and Structure for Protein Prediction Tasks.
CoRR, 2022
Proceedings of the 2022 SIAM International Conference on Data Mining, 2022
Proceedings of the Advances in Neural Information Processing Systems 35: Annual Conference on Neural Information Processing Systems 2022, 2022
Sequence-Structure Embeddings via Protein Language Models Improve on Prediction Tasks.
Proceedings of the IEEE International Conference on Knowledge Graph, 2022
Proceedings of the Artificial Neural Networks and Machine Learning - ICANN 2022, 2022
Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine, 2022
Equivariant Encoding based GVAE (EqEn-GVAE) for Protein Tertiary Structure Generation.
Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine, 2022
Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine, 2022
2021
Dataset for Disentangled Representation Learning for Interpretable Molecule Generation.
Dataset, April, 2021
Dataset for Space Partitioning and Regression Mode Seeking via a Mean-Shift-Inspired Algorithm.
Dataset, March, 2021
Dataset for Generative Adversarial Learning of Protein Tertiary Structures. Molecules, 2021.
Dataset, February, 2021
J. Bioinform. Comput. Biol., 2021
Traffic Flow Forecasting with Maintenance Downtime via Multi-Channel Attention-Based Spatio-Temporal Graph Convolutional Networks.
CoRR, 2021
CoRR, 2021
Proceedings of the Computational Advances in Bio and Medical Sciences: 11th International Conference, 2021
Single Model Quality Estimation of Protein Structures via Non-negative Tensor Factorization.
Proceedings of the Computational Advances in Bio and Medical Sciences: 11th International Conference, 2021
Proceedings of the Artificial Neural Networks and Machine Learning - ICANN 2021, 2021
PsychBERT: A Mental Health Language Model for Social Media Mental Health Behavioral Analysis.
Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine, 2021
Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine, 2021
Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine, 2021
Generating Physically-Realistic Tertiary Protein Structures with Deep Latent Variable Models Learning Over Experimentally-available Structures.
Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine, 2021
2020
Generating Tertiary Protein Structures via an Interpretative Variational Autoencoder.
CoRR, 2020
Decoy selection for protein structure prediction via extreme gradient boosting and ranking.
BMC Bioinform., 2020
A Multi-channel BiLSTM-CNN Model for Multilabel Emotion Classification of Informal Text.
Proceedings of the IEEE 14th International Conference on Semantic Computing, 2020
Reconstruction and Decomposition of High-Dimensional Landscapes via Unsupervised Learning.
Proceedings of the KDD '20: The 26th ACM SIGKDD Conference on Knowledge Discovery and Data Mining, 2020
Proceedings of the KDD '20: The 26th ACM SIGKDD Conference on Knowledge Discovery and Data Mining, 2020
Protein Decoy Generation via Adaptive Stochastic Optimization for Protein Structure Determination.
Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine, 2020
Decoy Selection in Protein Structure Determination via Symmetric Non-negative Matrix Factorization.
Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine, 2020
Proceedings of the BCB '20: 11th ACM International Conference on Bioinformatics, 2020
Proceedings of the BCB '20: 11th ACM International Conference on Bioinformatics, 2020
2019
Proceedings of the Innovations in Big Data Mining and Embedded Knowledge, 2019
Guest Editorial on the Special Issue on Informatics on Biomedical Data Learning, Reasoning, and Representation.
IEEE J. Biomed. Health Informatics, 2019
Guest Editorial for the ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics.
IEEE ACM Trans. Comput. Biol. Bioinform., 2019
Building maps of protein structure spaces in template-free protein structure prediction.
J. Bioinform. Comput. Biol., 2019
From molecular energy landscapes to equilibrium dynamics via landscape analysis and markov state models.
J. Bioinform. Comput. Biol., 2019
ROMEO: A Plug-and-play Software Platform of Robotics-inspired Algorithms for Modeling Biomolecular Structures and Motions.
CoRR, 2019
Balancing multiple objectives in conformation sampling to control decoy diversity in template-free protein structure prediction.
BMC Bioinform., 2019
BMC Bioinform., 2019
Proceedings of the Social, Cultural, and Behavioral Modeling, 2019
Proceedings of the Genetic and Evolutionary Computation Conference, 2019
Proceedings of the 2019 IEEE International Conference on Bioinformatics and Biomedicine, 2019
Non-Negative Matrix Factorization for Selection of Near-Native Protein Tertiary Structures.
Proceedings of the 2019 IEEE International Conference on Bioinformatics and Biomedicine, 2019
Using Sequence-Predicted Contacts to Guide Template-free Protein Structure Prediction.
Proceedings of the 10th ACM International Conference on Bioinformatics, 2019
Proceedings of the 10th ACM International Conference on Bioinformatics, 2019
Proceedings of the 10th ACM International Conference on Bioinformatics, 2019
2018
From Optimization to Mapping: An Evolutionary Algorithm for Protein Energy Landscapes.
IEEE ACM Trans. Comput. Biol. Bioinform., 2018
IEEE ACM Trans. Comput. Biol. Bioinform., 2018
Advances in the Application and Development of Non-Linear Global Optimization Techniques in Computational Structural Biology.
IEEE ACM Trans. Comput. Biol. Bioinform., 2018
J. Comput. Biol., 2018
An Energy Landscape Treatment of Decoy Selection in Template-Free Protein Structure Prediction.
Comput., 2018
Proceedings of the 8th IEEE International Conference on Computational Advances in Bio and Medical Sciences, 2018
Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine, 2018
Reconstructing and Decomposing Protein Energy Landscapes to Organize Structure Spaces and Reveal Biologically-active States.
Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine, 2018
Analysis of Molecular Structure Data]{Systematic Study of Different Design Decisions in Markov Model-based Analysis of Molecular Structure Data: Extended Abstract.
Proceedings of the 2018 ACM International Conference on Bioinformatics, 2018
Modeling Macromolecular Structures and Motions: Computational Methods for Sampling and Analysis of Energy Landscapes.
Proceedings of the 2018 ACM International Conference on Bioinformatics, 2018
Community Detection for Decoy Selection in Template-free Protein Structure Prediction.
Proceedings of the 2018 ACM International Conference on Bioinformatics, 2018
Modeling the Tertiary Structure of a Multi-domain Protein: Structure Prediction of Multi-domain Proteins.
Proceedings of the 2018 ACM International Conference on Bioinformatics, 2018
2017
IEEE ACM Trans. Comput. Biol. Bioinform., 2017
Improving Recognition of Antimicrobial Peptides and Target Selectivity through Machine Learning and Genetic Programming.
IEEE ACM Trans. Comput. Biol. Bioinform., 2017
Proceedings of the 7th IEEE International Conference on Computational Advances in Bio and Medical Sciences, 2017
Proceedings of the Genetic and Evolutionary Computation Conference, 2017
Proceedings of the Genetic and Evolutionary Computation Conference, 2017
Proceedings of the IEEE Conference on Computational Intelligence in Bioinformatics and Computational Biology, 2017
Proceedings of the 2017 IEEE International Conference on Bioinformatics and Biomedicine, 2017
Proceedings of the 8th ACM International Conference on Bioinformatics, 2017
Proceedings of the 8th ACM International Conference on Bioinformatics, 2017
Statistical Analysis of Computed Energy Landscapes to Understand Dysfunction in Pathogenic Protein Variants.
Proceedings of the 8th ACM International Conference on Bioinformatics, 2017
ACM-BCB '17 Tutorial: Robotics-inspired Algorithms for Modeling Protein Structures and Motions.
Proceedings of the 8th ACM International Conference on Bioinformatics, 2017
Proceedings of the 8th ACM International Conference on Bioinformatics, 2017
2016
Foreword on special issue on robotics methods for structural and dynamic modeling of molecular systems.
Robotica, 2016
Principles and Overview of Sampling Methods for Modeling Macromolecular Structure and Dynamics.
PLoS Comput. Biol., 2016
A Survey of Computational Treatments of Biomolecules by Robotics-Inspired Methods Modeling Equilibrium Structure and Dynamic.
J. Artif. Intell. Res., 2016
Path-based Guidance of an Evolutionary Algorithm in Mapping a Fitness Landscape and its Connectivity.
Proceedings of the Genetic and Evolutionary Computation Conference, 2016
A Novel EA-based Memetic Approach for Efficiently Mapping Complex Fitness Landscapes.
Proceedings of the 2016 on Genetic and Evolutionary Computation Conference, Denver, CO, USA, July 20, 2016
Workshop Evolutionary Computation in Computational Structural Biology 2016 Chairs' Welcome.
Proceedings of the Genetic and Evolutionary Computation Conference, 2016
Proceedings of the Genetic and Evolutionary Computation Conference, 2016
Proceedings of the 7th ACM International Conference on Bioinformatics, 2016
2015
Computational Methods for Exploration and Analysis of Macromolecular Structure and Dynamics.
PLoS Comput. Biol., 2015
Mapping the Conformation Space of Wildtype and Mutant H-Ras with a Memetic, Cellular, and Multiscale Evolutionary Algorithm.
PLoS Comput. Biol., 2015
idDock+: Integrating Machine Learning in Probabilistic Search for Protein-Protein Docking.
J. Comput. Biol., 2015
A Data-Driven Evolutionary Algorithm for Mapping Multibasin Protein Energy Landscapes.
J. Comput. Biol., 2015
Proceedings of the Bioinformatics Research and Applications - 11th International Symposium, 2015
Proceedings of the Genetic and Evolutionary Computation Conference, 2015
Proceedings of the Genetic and Evolutionary Computation Conference, 2015
Proceedings of the Genetic and Evolutionary Computation Conference, 2015
Evolutionary search strategies for efficient sample-based representations of multiple-basin protein energy landscapes.
Proceedings of the 2015 IEEE International Conference on Bioinformatics and Biomedicine, 2015
Computing transition paths in multiple-basin proteins with a probabilistic roadmap algorithm guided by structure data.
Proceedings of the 2015 IEEE International Conference on Bioinformatics and Biomedicine, 2015
2014
Exploring representations of protein structure for automated remote homology detection and mapping of protein structure space.
BMC Bioinform., 2014
Evolutionary search algorithms for protein modeling: from de novo structure prediction to comprehensive maps of functionally-relevant structures of protein chains and assemblies.
Proceedings of the Genetic and Evolutionary Computation Conference, 2014
A novel method to improve recognition of antimicrobial peptides through distal sequence-based features.
Proceedings of the 2014 IEEE International Conference on Bioinformatics and Biomedicine, 2014
Sampling-based methods for a full characterization of energy landscapes of small peptides.
Proceedings of the 2014 IEEE International Conference on Bioinformatics and Biomedicine, 2014
Knowledge-based search and multi-objective filters: proposed structural models of GPCR dimerization.
Proceedings of the 5th ACM Conference on Bioinformatics, 2014
A multiscale hybrid evolutionary algorithm to obtain sample-based representations of multi-basin protein energy landscapes.
Proceedings of the 5th ACM Conference on Bioinformatics, 2014
2013
Probabilistic Search and Energy Guidance for Biased Decoy Sampling in Ab Initio Protein Structure Prediction.
IEEE ACM Trans. Comput. Biol. Bioinform., 2013
Systematic analysis of global features and model building for recognition of antimicrobial peptides.
Proceedings of the IEEE 3rd International Conference on Computational Advances in Bio and Medical Sciences, 2013
Proceedings of the IEEE 3rd International Conference on Computational Advances in Bio and Medical Sciences, 2013
Proceedings of the Genetic and Evolutionary Computation Conference, 2013
Proceedings of the ACM Conference on Bioinformatics, 2013
Multi-Objective Stochastic Search for Sampling Local Minima in the Protein Energy Surface.
Proceedings of the ACM Conference on Bioinformatics, 2013
Proceedings of the ACM Conference on Bioinformatics, 2013
Proceedings of the ACM Conference on Bioinformatics, 2013
Proceedings of the ACM Conference on Bioinformatics, 2013
Proceedings of the ACM Conference on Bioinformatics, 2013
2012
An Evolutionary Algorithm Approach for Feature Generation from Sequence Data and Its Application to DNA Splice Site Prediction.
IEEE ACM Trans. Comput. Biol. Bioinform., 2012
Guiding Probabilistic Search of the protein conformational Space with Structural Profiles.
J. Bioinform. Comput. Biol., 2012
J. Bioinform. Comput. Biol., 2012
An Evolutionary conservation-Based Method for Refining and Reranking protein Complex Structures.
J. Bioinform. Comput. Biol., 2012
Basin Hopping as a General and Versatile Optimization Framework for the Characterization of Biological Macromolecules.
Adv. Artif. Intell., 2012
Proceedings of the Parallel Problem Solving from Nature - PPSN XII, 2012
Proceedings of the 2012 IEEE International Conference on Bioinformatics and Biomedicine Workshops, 2012
Proceedings of the 2012 IEEE International Conference on Bioinformatics and Biomedicine Workshops, 2012
A population-based evolutionary algorithm for sampling minima in the protein energy surface.
Proceedings of the 2012 IEEE International Conference on Bioinformatics and Biomedicine Workshops, 2012
Proceedings of the 2012 IEEE International Conference on Bioinformatics and Biomedicine Workshops, 2012
Proceedings of the 2012 IEEE International Conference on Bioinformatics and Biomedicine, 2012
Proceedings of the 2012 IEEE International Conference on Bioinformatics and Biomedicine Workshops, 2012
Proceedings of the 2012 IEEE International Conference on Bioinformatics and Biomedicine Workshops, 2012
A robotics-inspired method to sample conformational paths connecting known functionally-relevant structures in protein systems.
Proceedings of the 2012 IEEE International Conference on Bioinformatics and Biomedicine Workshops, 2012
Proceedings of the 2012 IEEE International Conference on Bioinformatics and Biomedicine Workshops, 2012
Proceedings of the 2012 IEEE International Conference on Bioinformatics and Biomedicine, 2012
An evolutionary search framework to efficiently sample local minima in the protein conformational space.
Proceedings of the ACM International Conference on Bioinformatics, 2012
Proceedings of the ACM International Conference on Bioinformatics, 2012
2011
J. Bioinform. Comput. Biol., 2011
A Two-Stage Evolutionary Approach for Effective Classification of hypersensitive DNA Sequences.
J. Bioinform. Comput. Biol., 2011
The 5th International Conference on Bio-Inspired Models of Network, Information and Computing Systems (Bionetics 2010) Special Track on Bioinformatics.
J. Bioinform. Comput. Biol., 2011
An evolutionary-based approach for feature generation: Eukaryotic promoter recognition.
Proceedings of the IEEE Congress on Evolutionary Computation, 2011
Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine, 2011
Proceedings of the 2011 IEEE International Conference on Bioinformatics and Biomedicine Workshops, 2011
Proceedings of the 2011 IEEE International Conference on Bioinformatics and Biomedicine Workshops, 2011
Proceedings of the 2011 IEEE International Conference on Bioinformatics and Biomedicine Workshops, 2011
Proceedings of the 2011 IEEE International Conference on Bioinformatics and Biomedicine Workshops, 2011
2010
Guiding the Search for Native-like Protein Conformations with an Ab-initio Tree-based Exploration.
Int. J. Robotics Res., 2010
Selecting predictive features for recognition of hypersensitive sites of regulatory genomic sequences with an evolutionary algorithm.
Proceedings of the Genetic and Evolutionary Computation Conference, 2010
Proceedings of the IEEE Congress on Evolutionary Computation, 2010
Proceedings of the Bio-Inspired Models of Network, Information, and Computing Systems, 2010
Feature and Kernel Evolution for Recognition of Hypersensitive Sites in DNA Sequences.
Proceedings of the Bio-Inspired Models of Network, Information, and Computing Systems, 2010
2009
An Ab-initio tree-based exploration to enhance sampling of low-energy protein conformations.
Proceedings of the Robotics: Science and Systems V, University of Washington, Seattle, USA, June 28, 2009
Proceedings of the Parallel Processing and Applied Mathematics, 2009
2007
Algorithmica, 2007