Toward a Detailed Description of the Thermally Induced Dynamics of the Core Promoter. - Boian S. Alexandrov; Vladimir Gelev; Sang Wook Yoo; Alan R. Bishop; Kim Ø. Rasmussen; Anny Usheva (PLoS Comput. Biol., 2009)

Binding of Nucleoid-Associated Protein Fis to DNA Is Regulated by DNA Breathing Dynamics. - Kristy Nowak-Lovato; Ludmil B. Alexandrov; Afsheen Banisadr; Amy L. Bauer; Alan R. Bishop; Anny Usheva; Fangping Mu; Elizabeth Hong-Geller; Kim Ø. Rasmussen; William S. Hlavacek; Boian S. Alexandrov (PLoS Comput. Biol., 2013)

The role of structural parameters in DNA cyclization. - Ludmil B. Alexandrov; Alan R. Bishop; Kim Ø. Rasmussen; Boian S. Alexandrov (BMC Bioinform., 2016)

Sources identification using shifted non-negative matrix factorization combined with semi-supervised clustering. - Filip L. Iliev; Valentin G. Stanev; Velimir V. Vesselinov; Boian S. Alexandrov (CoRR, 2016)

Machine learning approach for identification of release sources in advection-diffusion systems. - Valentin G. Stanev; Filip L. Iliev; Velimir V. Vesselinov; Boian S. Alexandrov (CoRR, 2016)

Nonnegative/binary matrix factorization with a D-Wave quantum annealer. - Daniel O'Malley; Velimir V. Vesselinov; Boian S. Alexandrov; Ludmil B. Alexandrov (CoRR, 2017)

Non-Negative Matrix Factorization for Selection of Near-Native Protein Tertiary Structures. - Nasrin Akhter; Raviteja Vangara; Gopinath Chennupati; Boian S. Alexandrov; Hristo N. Djidjev; Amarda Shehu (BIBM, 2019)

Nonnegative Canonical Polyadic Decomposition with Rank Deficient Factors. - Boian S. Alexandrov; Derek DeSantis; Gianmarco Manzini; Erik Skau (CoRR, 2019)

Unsupervised machine learning based on non-negative tensor factorization for analyzing reactive-mixing. - Velimir V. Vesselinov; Maruti Kumar Mudunuru; Satish Karra; Dan O'Malley; Boian S. Alexandrov (J. Comput. Phys., 2019)

Nonnegative tensor decomposition with custom clustering for microphase separation of block copolymers. - Boian S. Alexandrov; Valentin G. Stanev; Velimir V. Vesselinov; Kim Ø. Rasmussen (Stat. Anal. Data Min., 2019)

Decoy Selection in Protein Structure Determination via Symmetric Non-negative Matrix Factorization. - Kazi Lutful Kabir; Gopinath Chennupati; Raviteja Vangara; Hristo N. Djidjev; Boian S. Alexandrov; Amarda Shehu (BIBM, 2020)

Distributed Non-Negative Tensor Train Decomposition. - Manish Bhattarai; Gopinath Chennupati; Erik Skau; Raviteja Vangara; Hristo N. Djidjev; Boian S. Alexandrov (HPEC, 2020)

Semantic Nonnegative Matrix Factorization with Automatic Model Determination for Topic Modeling. - Raviteja Vangara; Erik Skau; Gopinath Chennupati; Hristo N. Djidjev; Thomas Tierney; James P. Smith; Manish Bhattarai; Valentin G. Stanev; Boian S. Alexandrov (ICMLA, 2020)

Tucker-1 Boolean Tensor Factorization with Quantum Annealers. - Daniel O'Malley; Hristo N. Djidjev; Boian S. Alexandrov (ICRC, 2020)

Multi-Dimensional Anomalous Entity Detection via Poisson Tensor Factorization. - Maksim Ekin Eren; Juston S. Moore; Boian S. Alexandrov (ISI, 2020)

An Out of Memory tSVD for Big-Data Factorization. - Hector Carrillo-Cabada; Erik Skau; Gopinath Chennupati; Boian S. Alexandrov; Hristo N. Djidjev (IEEE Access, 2020)

A Neural Network for Determination of Latent Dimensionality in Nonnegative Matrix Factorization. - Benjamin T. Nebgen; Raviteja Vangara; Miguel Ángel Hombrados-Herrera; Svetlana Kuksova; Boian S. Alexandrov (CoRR, 2020)

Identification of Anomalous Diffusion Sources by Unsupervised Learning. - Raviteja Vangara; Kim Ø. Rasmussen; Dimiter N. Petsev; Golan Bel; Boian S. Alexandrov (CoRR, 2020)

Factorizations of Binary Matrices - Rank Relations and the Uniqueness of Boolean Decompositions. - Derek DeSantis; Erik Skau; Boian S. Alexandrov (CoRR, 2020)

Coarse-grain cluster analysis of tensors with application to climate biome identification. - Derek DeSantis; Phillip J. Wolfram; Katrina Bennett; Boian S. Alexandrov (Mach. Learn. Sci. Technol., 2020)

Determination of latent dimensionality in international trade flow. - Duc Phan Minh Truong; Erik Skau; Vladimir I. Valtchinov; Boian S. Alexandrov (Mach. Learn. Sci. Technol., 2020)

Distributed non-negative matrix factorization with determination of the number of latent features. - Gopinath Chennupati; Raviteja Vangara; Erik Skau; Hristo N. Djidjev; Boian S. Alexandrov (J. Supercomput., 2020)

COVID-19 multidimensional kaggle literature organization. - Maksim Ekin Eren; Nick Solovyev 001; Chris Hamer; Renee McDonald; Boian S. Alexandrov; Charles Nicholas (DocEng, 2021)

Single Model Quality Estimation of Protein Structures via Non-negative Tensor Factorization. - Kazi Lutful Kabir; Manish Bhattarai; Boian S. Alexandrov; Amarda Shehu (ICCABS, 2021)

Boolean Hierarchical Tucker Networks on Quantum Annealers. - Elijah Pelofske; Georg Hahn; Daniel O'Malley; Hristo N. Djidjev; Boian S. Alexandrov (LSSC, 2021)

Topic Analysis of Superconductivity Literature by Semantic Non-negative Matrix Factorization. - Valentin G. Stanev; Erik Skau; Ichiro Takeuchi; Boian S. Alexandrov (LSSC, 2021)

Selection of Optimal Salient Time Steps by Non-negative Tucker Tensor Decomposition. - Jesus Pulido; John Patchett; Manish Bhattarai; Boian S. Alexandrov; James P. Ahrens (EuroVis (Short Papers), 2021)

Automatic Model Determination for Quaternion NMF. - Giancarlo Sanchez; Erik Skau; Boian S. Alexandrov (IEEE Access, 2021)

Boolean Matrix Factorization via Nonnegative Auxiliary Optimization. - Duc Phan Minh Truong; Erik Skau; Derek DeSantis; Boian S. Alexandrov (IEEE Access, 2021)

Finding the Number of Latent Topics With Semantic Non-Negative Matrix Factorization. - Raviteja Vangara; Manish Bhattarai; Erik Skau; Gopinath Chennupati; Hristo N. Djidjev; Thomas Tierney; James P. Smith; Valentin G. Stanev; Boian S. Alexandrov (IEEE Access, 2021)

Quantum Annealing Algorithms for Boolean Tensor Networks. - Elijah Pelofske; Georg Hahn; Daniel O'Malley; Hristo N. Djidjev; Boian S. Alexandrov (CoRR, 2021)

SeNMFk-SPLIT: large corpora topic modeling by semantic non-negative matrix factorization with automatic model selection. - Maksim Ekin Eren; Nick Solovyev 001; Manish Bhattarai; Kim Ø. Rasmussen; Charles Nicholas; Boian S. Alexandrov (DocEng, 2022)

Distributed Out-of-Memory SVD on CPU/GPU Architectures. - Ismael Boureima; Manish Bhattarai; Maksim Ekin Eren; Nick Solovyev 001; Hristo N. Djidjev; Boian S. Alexandrov (HPEC, 2022)

One-Shot Federated Group Collaborative Filtering. - Maksim Ekin Eren; Manish Bhattarai; Nicholas Solovyev 001; Luke E. Richards; Roberto Yus; Charles Nicholas; Boian S. Alexandrov (ICMLA, 2022)

Distributed non-negative RESCAL with Automatic Model Selection for Exascale Data. - Manish Bhattarai; Namita Kharat; Erik Skau; Benjamin T. Nebgen; Hristo N. Djidjev; Sanjay V. Rajopadhye; James P. Smith; Boian S. Alexandrov (CoRR, 2022)

Distributed Out-of-Memory NMF of Dense and Sparse Data on CPU/GPU Architectures with Automatic Model Selection for Exascale Data. - Ismael Boureima; Manish Bhattarai; Maksim Ekin Eren; Erik Skau; Philip Romero; Stephan J. Eidenbenz; Boian S. Alexandrov (CoRR, 2022)

FedSPLIT: One-Shot Federated Recommendation System Based on Non-negative Joint Matrix Factorization and Knowledge Distillation. - Maksim Ekin Eren; Luke E. Richards; Manish Bhattarai; Roberto Yus; Charles Nicholas; Boian S. Alexandrov (CoRR, 2022)

Process Modeling, Hidden Markov Models, and Non-negative Tensor Factorization with Model Selection. - Erik Skau; Andrew Hollis; Stephan J. Eidenbenz; Kim Ø. Rasmussen; Boian S. Alexandrov (CoRR, 2022)

Nonnegative canonical tensor decomposition with linear constraints: nnCANDELINC. - Boian S. Alexandrov; Derek F. DeSantis; Gianmarco Manzini; Erik W. Skau (Numer. Linear Algebra Appl., 2022)

Improved Protein Decoy Selection via Non-Negative Matrix Factorization. - Nasrin Akhter; Kazi Lutful Kabir; Gopinath Chennupati; Raviteja Vangara; Boian S. Alexandrov; Hristo N. Djidjev; Amarda Shehu (IEEE ACM Trans. Comput. Biol. Bioinform., 2022)

Factorization of Binary Matrices: Rank Relations, Uniqueness and Model Selection of Boolean Decomposition. - Derek DeSantis; Erik Skau; Duc Phan Minh Truong; Boian S. Alexandrov (ACM Trans. Knowl. Discov. Data, 2022)

Robust Adversarial Defense by Tensor Factorization. - Manish Bhattarai; Mehmet Cagri Kaymak; Ryan Barron; Ben Nebgen; Kim Ø. Rasmussen; Boian S. Alexandrov (ICMLA, 2023)

Interactive Distillation of Large Single-Topic Corpora of Scientific Papers. - Nicholas Solovyev 001; Ryan Barron; Manish Bhattarai; Maksim Ekin Eren; Kim Ø. Rasmussen; Boian S. Alexandrov (ICMLA, 2023)

MalwareDNA: Simultaneous Classification of Malware, Malware Families, and Novel Malware. - Maksim Ekin Eren; Manish Bhattarai; Kim Ø. Rasmussen; Boian S. Alexandrov; Charles Nicholas (ISI, 2023)

Electrical Grid Anomaly Detection via Tensor Decomposition. - Alexander Most; Maksim Ekin Eren; Boian S. Alexandrov; Nigel Lawrence (MILCOM, 2023)

Tensor Networks for Solving Realistic Time-independent Boltzmann Neutron Transport Equation. - Duc P. Truong; Mario I. Ortega; Ismael Boureima; Gianmarco Manzini; Kim Ø. Rasmussen; Boian S. Alexandrov (CoRR, 2023)

General-purpose Unsupervised Cyber Anomaly Detection via Non-negative Tensor Factorization. - Maksim Ekin Eren; Juston S. Moore; Erik Skau; Elisabeth Moore; Manish Bhattarai; Gopinath Chennupati; Boian S. Alexandrov (DTRAP, 2023)

The tensor-train mimetic finite difference method for three-dimensional Maxwell's wave propagation equations. - Gianmarco Manzini; Duc Phan Minh Truong; Radoslav G. Vuchkov; Boian S. Alexandrov (Math. Comput. Simul., 2023)

Distributed non-negative RESCAL with automatic model selection for exascale data. - Manish Bhattarai; Namita Kharat; Ismael Boureima; Erik Skau; Benjamin T. Nebgen; Hristo N. Djidjev; Sanjay V. Rajopadhye; James P. Smith; Boian S. Alexandrov (J. Parallel Distributed Comput., 2023)

Examining DNA breathing with pyDNA-EPBD. - Anowarul Kabir; Manish Bhattarai; Kim Ø. Rasmussen; Amarda Shehu; Anny Usheva; Alan R. Bishop; Boian S. Alexandrov (Bioinform., 2023)

Semi-Supervised Classification of Malware Families Under Extreme Class Imbalance via Hierarchical Non-Negative Matrix Factorization with Automatic Model Selection. - Maksim Ekin Eren; Manish Bhattarai; Robert J. Joyce; Edward Raff; Charles Nicholas; Boian S. Alexandrov (ACM Trans. Priv. Secur., 2023)

TopicTag: Automatic Annotation of NMF Topic Models Using Chain of Thought and Prompt Tuning with LLMs. - Selma Wanna; Nicholas Solovyev 001; Ryan Barron; Maksim Ekin Eren; Manish Bhattarai; Kim Ø. Rasmussen; Boian S. Alexandrov (DocEng, 2024)

Binary Bleed: Fast Distributed and Parallel Method for Automatic Model Selection. - Ryan Barron; Maksim Ekin Eren; Manish Bhattarai; Ismael Boureima; Cynthia Matuszek; Boian S. Alexandrov (HPEC, 2024)

Enhancing Code Translation in Language Models with Few-Shot Learning via Retrieval-Augmented Generation. - Manish Bhattarai; Javier E. Santos; Shawn Jones; Ayan Biswas; Boian S. Alexandrov; Daniel O'Malley (HPEC, 2024)

Tensor Train Low-rank Approximation (TT-LoRA): Democratizing AI with Accelerated LLMs. - Afia Anjum; Maksim Ekin Eren; Ismael Boureima; Boian S. Alexandrov; Manish Bhattarai (ICMLA, 2024)

Domain-Specific Retrieval-Augmented Generation Using Vector Stores, Knowledge Graphs, and Tensor Factorization. - Ryan Barron; Ves Grantcharov; Selma Wanna; Maksim Ekin Eren; Manish Bhattarai; Nicholas Solovyev 001; George Tompkins; Charles Nicholas; Kim Ø. Rasmussen; Cynthia Matuszek; Boian S. Alexandrov (ICMLA, 2024)

Cyber-Security Knowledge Graph Generation by Hierarchical Nonnegative Matrix Factorization. - Ryan Barron; Maksim Ekin Eren; Manish Bhattarai; Selma Wanna; Nick Solovyev 001; Kim Ø. Rasmussen; Boian S. Alexandrov; Charles Nicholas; Cynthia Matuszek (ISDFS, 2024)

Catch'em all: Classification of Rare, Prominent, and Novel Malware Families. - Maksim Ekin Eren; Ryan Barron; Manish Bhattarai; Selma Wanna; Nicholas Solovyev 001; Kim Ø. Rasmussen; Boian S. Alexandrov; Charles Nicholas (ISDFS, 2024)

Tensor Network Space-Time Spectral Collocation Method for Time Dependent Convection-Diffusion-Reaction Equations. - Dibyendu Adak; Duc P. Truong; Gianmarco Manzini; Kim Ø. Rasmussen; Boian S. Alexandrov (CoRR, 2024)

High-order Tensor-Train Finite Volume Method for Shallow Water Equations. - Mustafa Engin Danis; Duc P. Truong; Derek DeSantis; Mark Petersen; Kim Ø. Rasmussen; Boian S. Alexandrov (CoRR, 2024)

LaFA: Latent Feature Attacks on Non-negative Matrix Factorization. - Minh N. Vu; Ben Nebgen; Erik Skau; Geigh Zollicoffer; Juan Castorena; Kim Ø. Rasmussen; Boian S. Alexandrov; Manish Bhattarai (CoRR, 2024)

Space-Time Spectral Element Tensor Network Approach for Time Dependent Convection Diffusion Reaction Equation with Variable Coefficients. - Dibyendu Adak; Duc P. Truong; Radoslav G. Vuchkov; Saibal De; Derek DeSantis; Nathan V. Roberts; Kim Ø. Rasmussen; Boian S. Alexandrov (CoRR, 2024)

HEAL: Hierarchical Embedding Alignment Loss for Improved Retrieval and Representation Learning. - Manish Bhattarai; Ryan Barron; Maksim Ekin Eren; Minh Vu; Ves Grantcharov; Ismael Boureima; Valentin G. Stanev; Cynthia Matuszek; Vladimir I. Valtchinov; Kim Ø. Rasmussen; Boian S. Alexandrov (CoRR, 2024)

Tensor networks for solving the time-independent Boltzmann neutron transport equation. - Duc P. Truong; Mario I. Ortega; Ismael Boureima; Gianmarco Manzini; Kim Ø. Rasmussen; Boian S. Alexandrov (J. Comput. Phys., 2024)

Distributed out-of-memory NMF on CPU/GPU architectures. - Ismael Boureima; Manish Bhattarai; Maksim Ekin Eren; Erik Skau; Philip Romero; Stephan J. Eidenbenz; Boian S. Alexandrov (J. Supercomput., 2024)

Correction to: Distributed out-of-memory NMF on CPU/GPU architectures. - Ismael Boureima; Manish Bhattarai; Maksim Ekin Eren; Erik Skau; Philip Romero; Stephan J. Eidenbenz; Boian S. Alexandrov (J. Supercomput., 2024)

Generating Hidden Markov Models from Process Models Through Nonnegative Tensor Factorization. - Erik Skau; Andrew Hollis; Stephan J. Eidenbenz; Kim Ø. Rasmussen; Boian S. Alexandrov (ACM Trans. Model. Comput. Simul., 2024)

LoRID: Low-Rank Iterative Diffusion for Adversarial Purification. - Geigh Zollicoffer; Minh N. Vu; Ben Nebgen; Juan Castorena; Boian S. Alexandrov; Manish Bhattarai (AAAI, 2025)

Tensor-train WENO scheme for compressible flows. - Mustafa Engin Danis; Duc P. Truong; Ismael Boureima; Oleg Korobkin; Kim Ø. Rasmussen; Boian S. Alexandrov (J. Comput. Phys., 2025)

Specificity and tunability of efflux pumps: A new role for the proton gradient? - Matthew Gerry; Duncan Kirby; Boian S. Alexandrov; Dvira Segal; Anton Zilman (PLoS Comput. Biol., 2025)

Topological Signatures of Adversaries in Multimodal Alignments. - Minh N. Vu; Geigh Zollicoffer; Huy Mai; Ben Nebgen; Boian S. Alexandrov; Manish Bhattarai (CoRR, 2025)

Bridging Legal Knowledge and AI: Retrieval-Augmented Generation with Vector Stores, Knowledge Graphs, and Hierarchical Non-negative Matrix Factorization. - Ryan Barron; Maksim Ekin Eren; Olga M. Serafimova; Cynthia Matuszek; Boian S. Alexandrov (CoRR, 2025)

Matrix Factorization for Inferring Associations and Missing Links. - Ryan Barron; Maksim Ekin Eren; Duc P. Truong; Cynthia Matuszek; James Wendelberger; Mary F. Dorn; Boian S. Alexandrov (CoRR, 2025)

Tensor Network Space-Time Spectral Collocation Method for Solving the Nonlinear Convection Diffusion Equation. - Dibyendu Adak; Mustafa Engin Danis; Duc P. Truong; Kim Ø. Rasmussen; Boian S. Alexandrov (J. Sci. Comput., 2025)

Topic Modeling and Link-Prediction for Material Property Discovery. - Ryan Barron; Maksim Ekin Eren; Valentin G. Stanev; Cynthia Matuszek; Boian S. Alexandrov (CoRR, 2025)