Amarda Shehu

ORCID

Publication Activity (10 Years)

Years Active: 2007-2024
Publications (10 Years): 91

Top Venues

Publications

Toki Tahmid Inan, Amarda Shehu
Revisiting Evolutionary Algorithms for Optimization for Deep Learning: Introducing DL-HEA: EAs for Optimization for Deep Learning. GECCO Companion (2024)
Yuanjie Lu, Amarda Shehu, David Lattanzi
Accounting for Work Zone Disruptions in Traffic Flow Forecasting. CoRR (2024)
Toki Tahmid Inan, Mingrui Liu, Amarda Shehu
Beyond Single-Model Views for Deep Learning: Optimization versus Generalizability of Stochastic Optimization Algorithms. CoRR (2024)
Megan Herceg, Amarda Shehu
Structure- and Energy-based Analysis of Small Molecule Ligand Binding to Steroid Nuclear Receptors. BCB (2023)
Anowarul Kabir, Manish Bhattarai, Kim Ø. Rasmussen, Amarda Shehu, Anny Usheva, Alan R. Bishop, Boian S. Alexandrov
Examining DNA breathing with pyDNA-EPBD. Bioinform. 39 (10) (2023)
Yajie Bao, Amarda Shehu, Mingrui Liu
Global Convergence Analysis of Local SGD for Two-layer Neural Network without Overparameterization. NeurIPS (2023)
Anowarul Kabir, Asher Moldwin, Amarda Shehu
A Comparative Analysis of Transformer-based Protein Language Models for Remote Homology Prediction. BCB (2023)
Ahmed Bin Zaman, Toki Tahmid Inan, Kenneth A. De Jong, Amarda Shehu
Adaptive Stochastic Optimization to Improve Protein Conformation Sampling. IEEE ACM Trans. Comput. Biol. Bioinform. 20 (5) (2023)
Shiyu Wang, Xiaojie Guo, Xuanyang Lin, Bo Pan, Yuanqi Du, Yinkai Wang, Yanfang Ye, Ashley Ann Petersen, Austin Leitgeb, Saleh AlKhalifa, Kevin Minbiole, William Wuest, Amarda Shehu, Liang Zhao
Multi-objective Deep Data Generation with Correlated Property Control. CoRR (2022)
Nasrin Akhter, Kazi Lutful Kabir, Gopinath Chennupati, Raviteja Vangara, Boian S. Alexandrov, Hristo N. Djidjev, Amarda Shehu
Improved Protein Decoy Selection via Non-Negative Matrix Factorization. IEEE ACM Trans. Comput. Biol. Bioinform. 19 (3) (2022)
Yuanqi Du, Xiaojie Guo, Amarda Shehu, Liang Zhao
Interpretable Molecular Graph Generation via Monotonic Constraints. CoRR (2022)
Anowarul Kabir, Amarda Shehu
Sequence-Structure Embeddings via Protein Language Models Improve on Prediction Tasks. ICKG (2022)
Parastoo Kamranfar, David Lattanzi, Amarda Shehu, Daniel Barbará
Multiple Instance Learning for Detecting Anomalies over Sequential Real-World Datasets. CoRR (2022)
Yuanqi Du, Xiaojie Guo, Amarda Shehu, Liang Zhao
Interpretable Molecular Graph Generation via Monotonic Constraints. SDM (2022)
Bo Pan, Yinkai Wang, Xuanyang Lin, Muran Qin, Yuanqi Du, Shiva Ghaemi, Aowei Ding, Shiyu Wang, Saleh AlKhalifa, Kevin Minbiole, William Wuest, Ashley Ann Petersen, Austin Leitgeb, Amarda Shehu, Liang Zhao
Property-Controllable Generation of Quaternary Ammonium Compounds. BIBM (2022)
Taseef Rahman, Fardina Fathmiul Alam, Amarda Shehu
Equivariant Encoding based GVAE (EqEn-GVAE) for Protein Tertiary Structure Generation. BIBM (2022)
Yuanqi Du, Xiaojie Guo, Yinkai Wang, Amarda Shehu, Liang Zhao
Small molecule generation via disentangled representation learning. Bioinform. 38 (12) (2022)
Shiyu Wang, Xiaojie Guo, Xuanyang Lin, Bo Pan, Yuanqi Du, Yinkai Wang, Yanfang Ye, Ashley Petersen, Austin Leitgeb, Saleh Alkhalifa, Kevin Minbiole, William M. Wuest, Amarda Shehu, Liang Zhao
Multi-objective Deep Data Generation with Correlated Property Control. NeurIPS (2022)
Anowarul Kabir, Amarda Shehu
Transformer Neural Networks Attending to Both Sequence and Structure for Protein Prediction Tasks. CoRR (2022)
Toki Tahmid Inan, Mingrui Liu, Amarda Shehu
F-Measure Optimization for Multi-class, Imbalanced Emotion Classification Tasks. ICANN (1) (2022)
Parastoo Kamranfar, David Lattanzi, Amarda Shehu, Shelley Stoffels
Pavement Distress Recognition via Wavelet-Based Clustering of Smartphone Accelerometer Data. J. Comput. Civ. Eng. 36 (4) (2022)
Yinkai Wang, Shiva Ghaemi, Aowei Ding, Yuanqui Du, Bo Pan, Muran Qin, Xuanyang Lin, Ashley Ann Petersen, Austin Leitgeb, Saleh AlKhalifa, Kevin Minbiole, William Wuest, Liang Zhao, Amarda Shehu
Generation and Characterization of Quaternary Ammonium Compounds via Deep Learning. BIBM (2022)
Zahra Rajabi, Özlem Uzuner, Amarda Shehu
Detecting Scarce Emotions Using BERT and Hyperparameter Optimization. ICANN (5) (2021)
Vedant Vajre, Mitchell Naylor, Uday Kamath, Amarda Shehu
PsychBERT: A Mental Health Language Model for Social Media Mental Health Behavioral Analysis. BIBM (2021)
Yuanqi Du, Yinkai Wang, Fardina Fathmiul Alam, Yuanjie Lu, Xiaojie Guo, Liang Zhao, Amarda Shehu
Deep Latent-Variable Models for Controllable Molecule Generation. BIBM (2021)
Wanli Qiao, Amarda Shehu
Space Partitioning and Regression Mode Seeking via a Mean-Shift-Inspired Algorithm. CoRR (2021)
Kazi Lutful Kabir, Ruth Nussinov, Buyong Ma, Amarda Shehu
Antigen Binding Reshapes Antibody Energy Landscape and Conformation Dynamics. BIBM (2021)
Fardina Fathmiul Alam, Amarda Shehu
Generating Physically-Realistic Tertiary Protein Structures with Deep Latent Variable Models Learning Over Experimentally-available Structures. BIBM (2021)
Taseef Rahman, Yuanqi Du, Amarda Shehu
Graph Representation Learning for Protein Conformation Sampling. ICCABS (2021)
Fardina Fathmiul Alam, Amarda Shehu
Unsupervised multi-instance learning for protein structure determination. J. Bioinform. Comput. Biol. 19 (1) (2021)
Yuanjie Lu, Parastoo Kamranfar, David Lattanzi, Amarda Shehu
Traffic Flow Forecasting with Maintenance Downtime via Multi-Channel Attention-Based Spatio-Temporal Graph Convolutional Networks. CoRR (2021)
Kazi Lutful Kabir, Manish Bhattarai, Boian S. Alexandrov, Amarda Shehu
Single Model Quality Estimation of Protein Structures via Non-negative Tensor Factorization. ICCABS (2021)
Nasrin Akhter, Gopinath Chennupati, Hristo N. Djidjev, Amarda Shehu
Decoy selection for protein structure prediction via extreme gradient boosting and ranking. BMC Bioinform. (1) (2020)
Zahra Rajabi, Amarda Shehu, Özlem Uzuner
A Multi-channel BiLSTM-CNN Model for Multilabel Emotion Classification of Informal Text. ICSC (2020)
Kazi Lutful Kabir, Gopinath Chennupati, Raviteja Vangara, Hristo N. Djidjev, Boian S. Alexandrov, Amarda Shehu
Decoy Selection in Protein Structure Determination via Symmetric Non-negative Matrix Factorization. BIBM (2020)
Xiaojie Guo, Liang Zhao, Zhao Qin, Lingfei Wu, Amarda Shehu, Yanfang Ye
Interpretable Deep Graph Generation with Node-edge Co-disentanglement. KDD (2020)
Xiaojie Guo, Liang Zhao, Zhao Qin, Lingfei Wu, Amarda Shehu, Yanfang Ye
Interpretable Deep Graph Generation with Node-Edge Co-Disentanglement. CoRR (2020)
Ahmed Bin Zaman, Toki Tahmid Inan, Amarda Shehu
Protein Decoy Generation via Adaptive Stochastic Optimization for Protein Structure Determination. BIBM (2020)
Xiaojie Guo, Sivani Tadepalli, Liang Zhao, Amarda Shehu
Generating Tertiary Protein Structures via an Interpretative Variational Autoencoder. CoRR (2020)
Jing Lei, Nasrin Akhter, Wanli Qiao, Amarda Shehu
Reconstruction and Decomposition of High-Dimensional Landscapes via Unsupervised Learning. KDD (2020)
Xiao Chen, Nasrin Akhter, Zhiye Guo, Tianqi Wu, Jie Hou, Amarda Shehu, Jianlin Cheng
Deep Ranking in Template-free Protein Structure Prediction. BCB (2020)
Nasrin Akhter, Gopinath Chennupati, Hristo N. Djidjev, Amarda Shehu
Decoy Selection for Protein Structure Prediction Via Extreme Gradient Boosting and Ranking. CoRR (2020)
Fardina Fathmiul Alam, Amarda Shehu
Variational Autoencoders for Protein Structure Prediction. BCB (2020)
Ahmed Bin Zaman, Parastoo Kamranfar, Carlotta Domeniconi, Amarda Shehu
Decoy Ensemble Reduction in Template-free Protein Structure Prediction. BCB (2019)
Fardina Fathmiul Alam, Taseef Rahman, Amarda Shehu
Learning Reduced Latent Representations of Protein Structure Data. BCB (2019)
Sivani Tadepalli, Nasrin Akhter, Daniel Barbará, Amarda Shehu
Identifying Near-Native Protein Structures via Anomaly Detection. BIBM (2019)
Ahmed Bin Zaman, Amarda Shehu
Building maps of protein structure spaces in template-free protein structure prediction. J. Bioinform. Comput. Biol. 17 (6) (2019)
Ahmed Bin Zaman, Kenneth A. De Jong, Amarda Shehu
Using subpopulation EAs to map molecular structure landscapes. GECCO (2019)
Kazi Lutful Kabir, Nasrin Akhter, Amarda Shehu
From molecular energy landscapes to equilibrium dynamics via landscape analysis and markov state models. J. Bioinform. Comput. Biol. 17 (6) (2019)
Tamer Kahveci, Giuseppe Pozzi, Amarda Shehu, May Dongmei Wang
Guest Editorial on the Special Issue on Informatics on Biomedical Data Learning, Reasoning, and Representation. IEEE J. Biomed. Health Informatics 23 (1) (2019)
David Morris, Tatiana Maximova, Erion Plaku, Amarda Shehu
Attenuating dependence on structural data in computing protein energy landscapes. BMC Bioinform. (11) (2019)
Ahmed Bin Zaman, Prasanna Venkatesh Parthasarathy, Amarda Shehu
Using Sequence-Predicted Contacts to Guide Template-free Protein Structure Prediction. BCB (2019)
Kevin Molloy, Erion Plaku, Amarda Shehu
ROMEO: A Plug-and-play Software Platform of Robotics-inspired Algorithms for Modeling Biomolecular Structures and Motions. CoRR (2019)
Amarda Shehu, Giuseppe Pozzi, Tamer Kahveci
Guest Editorial for the ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics. IEEE ACM Trans. Comput. Biol. Bioinform. 16 (5) (2019)
Ahmed Bin Zaman, Amarda Shehu
Balancing multiple objectives in conformation sampling to control decoy diversity in template-free protein structure prediction. BMC Bioinform. 20 (1) (2019)
Zahra Rajabi, Amarda Shehu, Hemant Purohit
User Behavior Modelling for Fake Information Mitigation on Social Web. SBP-BRiMS (2019)
Nasrin Akhter, Raviteja Vangara, Gopinath Chennupati, Boian S. Alexandrov, Hristo N. Djidjev, Amarda Shehu
Non-Negative Matrix Factorization for Selection of Near-Native Protein Tertiary Structures. BIBM (2019)
Nasrin Akhter, Gopinath Chennupati, Hristo N. Djidjev, Amarda Shehu
Improved Decoy Selection via Machine Learning and Ranking. ICCABS (2018)
Tatiana Maximova, Zijing Zhang, Daniel Carr, Erion Plaku, Amarda Shehu
Sample-Based Models of Protein Energy Landscapes and Slow Structural Rearrangements. J. Comput. Biol. 25 (1) (2018)
Julia Handl, Amarda Shehu, José Santos Reyes
Advances in the Application and Development of Non-Linear Global Optimization Techniques in Computational Structural Biology. IEEE ACM Trans. Comput. Biol. Bioinform. 15 (3) (2018)
Nasrin Akhter, Jing Lei, Wanli Qiao, Amarda Shehu
Reconstructing and Decomposing Protein Energy Landscapes to Organize Structure Spaces and Reveal Biologically-active States. BIBM (2018)
Liban Hassan, Zahra Rajabi, Nasrin Akhter, Amarda Shehu
Community Detection for Decoy Selection in Template-free Protein Structure Prediction. BCB (2018)
Sharmila Roychoudhury, Amarda Shehu
Analysis of Molecular Structure Data]{Systematic Study of Different Design Decisions in Markov Model-based Analysis of Molecular Structure Data: Extended Abstract. BCB (2018)
Nasrin Akhter, Wanli Qiao, Amarda Shehu
An Energy Landscape Treatment of Decoy Selection in Template-Free Protein Structure Prediction. Comput. 6 (2) (2018)
Daniel Veltri, Uday Kamath, Amarda Shehu
Deep learning improves antimicrobial peptide recognition. Bioinform. 34 (16) (2018)
Emmanuel Sapin, Kenneth A. De Jong, Amarda Shehu
From Optimization to Mapping: An Evolutionary Algorithm for Protein Energy Landscapes. IEEE ACM Trans. Comput. Biol. Bioinform. 15 (3) (2018)
Tatiana Maximova, Erion Plaku, Amarda Shehu
Structure-Guided Protein Transition Modeling with a Probabilistic Roadmap Algorithm. IEEE ACM Trans. Comput. Biol. Bioinform. 15 (6) (2018)
Kevin Molloy, Nasrin Akhter, Amarda Shehu
Modeling Macromolecular Structures and Motions: Computational Methods for Sampling and Analysis of Energy Landscapes. BCB (2018)
Fahad Almsned, Gideon Gogovi, Nicole Bracci, Kylene Kehn-Hall, Estela Blaisten-Barojas, Amarda Shehu
Modeling the Tertiary Structure of a Multi-domain Protein: Structure Prediction of Multi-domain Proteins. BCB (2018)
Manpriya Dua, Daniel Veltri, Barney Bishop, Amarda Shehu
Guiding Exploration of Antimicrobial Peptide Space with a Deep Neural Network. BIBM (2018)
Kevin Molloy, David Morris, Amarda Shehu
ACM-BCB '17 Tutorial: Robotics-inspired Algorithms for Modeling Protein Structures and Motions. BCB (2017)
David Morris, Tatiana Maximova, Erion Plaku, Amarda Shehu
Out of one, many: Exploiting intrinsic motions to explore protein structure spaces. ICCABS (2017)
Wanli Qiao, Tatiana Maximova, Xiaowen Fang, Erion Plaku, Amarda Shehu
Reconstructing and mining protein energy landscape to understand disease. BIBM (2017)
Emmanuel Sapin, Kenneth A. De Jong, Amarda Shehu
Evolutionary search for paths on protein energy landscapes. GECCO (Companion) (2017)
Emmanuel Sapin, Kenneth A. De Jong, Amarda Shehu
An evolutionary algorithm to model structural excursions of a protein. GECCO (Companion) (2017)
Emmanuel Sapin, Kenneth A. De Jong, Amarda Shehu
Evolving Conformation Paths to Model Protein Structural Transitions. BCB (2017)
Nurit Haspel, Amarda Shehu, Kevin Molloy
The 2017 Computational Structural Bioinformatics Workshop: CSBW 2017. BCB (2017)
Emmanuel Sapin, Kenneth A. De Jong, Amarda Shehu
Modeling protein structural transitions as a multiobjective optimization problem. CIBCB (2017)
Wanli Qiao, Tatiana Maximova, Erion Plaku, Amarda Shehu
Statistical Analysis of Computed Energy Landscapes to Understand Dysfunction in Pathogenic Protein Variants. BCB (2017)
Daniel Veltri, Uday Kamath, Amarda Shehu
Improving Recognition of Antimicrobial Peptides and Target Selectivity through Machine Learning and Genetic Programming. IEEE ACM Trans. Comput. Biol. Bioinform. 14 (2) (2017)
Illhoi Yoo, Amarda Shehu
Guest Editorial for Special Section on BIBM 2014. IEEE ACM Trans. Comput. Biol. Bioinform. 14 (2) (2017)
Amarda Shehu, Tamer Kahveci, Giuseppe Pozzi
Highlights Talks at ACM BCB 2017. BCB (2017)
Emmanuel Sapin, Kenneth A. De Jong, Amarda Shehu
A Novel EA-based Memetic Approach for Efficiently Mapping Complex Fitness Landscapes. GECCO (2016)
José Santos, Julia Handl, Amarda Shehu
Workshop Evolutionary Computation in Computational Structural Biology 2016 Chairs' Welcome. GECCO (Companion) (2016)
Amarda Shehu, Erion Plaku
A Survey of Computational Treatments of Biomolecules by Robotics-Inspired Methods Modeling Equilibrium Structure and Dynamic. J. Artif. Intell. Res. 57 (2016)
Carola Doerr, Julia Handl, Emma Hart, Gabriela Ochoa, Amarda Shehu, Tea Tusar, Anya E. Vostinar, Christine Zarges, A. Nur Zincir-Heywood
Women@GECCO 2016 Chairs' Welcome. GECCO (Companion) (2016)
Lydia Tapia, Juan Cortés, Amarda Shehu, Jinalin Chen
Foreword on special issue on robotics methods for structural and dynamic modeling of molecular systems. Robotica 34 (8) (2016)
Tatiana Maximova, Daniel Carr, Erion Plaku, Amarda Shehu
Sample-based Models of Protein Structural Transitions. BCB (2016)
Kevin Molloy, Rudy Clausen, Amarda Shehu
A stochastic roadmap method to model protein structural transitions. Robotica 34 (8) (2016)
Tatiana Maximova, Ryan Moffatt, Buyong Ma, Ruth Nussinov, Amarda Shehu
Principles and Overview of Sampling Methods for Modeling Macromolecular Structure and Dynamics. PLoS Comput. Biol. 12 (4) (2016)
Emmanuel Sapin, Kenneth A. De Jong, Amarda Shehu
Path-based Guidance of an Evolutionary Algorithm in Mapping a Fitness Landscape and its Connectivity. GECCO (Companion) (2016)
Rudy Clausen, Buyong Ma, Ruth Nussinov, Amarda Shehu
Mapping the Conformation Space of Wildtype and Mutant H-Ras with a Memetic, Cellular, and Multiscale Evolutionary Algorithm. PLoS Comput. Biol. 11 (9) (2015)
Emmanuel Sapin, Kenneth A. De Jong, Amarda Shehu
Evolutionary search strategies for efficient sample-based representations of multiple-basin protein energy landscapes. BIBM (2015)
Rudy Clausen, Amarda Shehu
A Data-Driven Evolutionary Algorithm for Mapping Multibasin Protein Energy Landscapes. J. Comput. Biol. 22 (9) (2015)
Emmanuel Sapin, Kenneth A. De Jong, Amarda Shehu
Mapping Multiple Minima in Protein Energy Landscapes with Evolutionary Algorithms. GECCO (Companion) (2015)
Amarda Shehu, Ruth Nussinov
Computational Methods for Exploration and Analysis of Macromolecular Structure and Dynamics. PLoS Comput. Biol. 11 (10) (2015)
Tatiana Maximova, Erion Plaku, Amarda Shehu
Computing transition paths in multiple-basin proteins with a probabilistic roadmap algorithm guided by structure data. BIBM (2015)
Amarda Shehu, Kenneth A. De Jong
Evolutionary Algorithms for Protein Structure Modeling. GECCO (Companion) (2015)
Rudy Clausen, Emmanuel Sapin, Kenneth A. De Jong, Amarda Shehu
Evolution Strategies for Exploring Protein Energy Landscapes. GECCO (2015)
Irina Hashmi, Amarda Shehu
idDock+: Integrating Machine Learning in Probabilistic Search for Protein-Protein Docking. J. Comput. Biol. 22 (9) (2015)

Amarda Shehu.css-eqlu8i{font-size:small;padding-left:4px;}

Publication Activity (10 Years)

Top Topics

Top Venues

Amarda Shehu