Designing fast converging phylogenetic methods. - Luay Nakhleh; Usman Roshan; Katherine St. John; Jerry Sun 001; Tandy J. Warnow (ISMB (Supplement of Bioinformatics), 2001)

The Performance of Phylogenetic Methods on Trees of Bounded Diameter. - Luay Nakhleh; Usman Roshan; Katherine St. John; Jerry Sun 001; Tandy J. Warnow (WABI, 2001)

The Accuracy of Fast Phylogenetic Methods for Large Datasets. - Luay Nakhleh; Bernard M. E. Moret; Usman Roshan; Katherine St. John; Jerry Sun 001; Tandy J. Warnow (Pacific Symposium on Biocomputing, 2002)

Sequence-Length Requirements for Phylogenetic Methods. - Bernard M. E. Moret; Usman Roshan; Tandy J. Warnow (WABI, 2002)

Estimating the Deviation from a Molecular Clock. - Luay Nakhleh; Usman Roshan; Lisa Vawter; Tandy J. Warnow (WABI, 2002)

Diametrical clustering for identifying anti-correlated gene clusters. - Inderjit S. Dhillon; Edward M. Marcotte; Usman Roshan (Bioinform., 2003)

Rec-I-DCM3: A Fast Algorithmic Technique for Reconstructing Large Phylogenetic Trees. - Usman Roshan; Bernard M. E. Moret; Tandy J. Warnow; Tiffani L. Williams (CSB, 2004)

Improved Phylogenetic Motif Detection Using Parsimony. - Usman Roshan; Dennis R. Livesay; David La (BIBE, 2005)

Parallel Divide-and-Conquer Phylogeny Reconstruction by Maximum Likelihood. - Z. Du; Alexandros Stamatakis; F. Lin; Usman Roshan; Luay Nakhleh (HPCC, 2005)

Reconstruction of large phylogenetic trees: A parallel approach. - Zhihua Du; Feng Lin; Usman W. Roshan (Comput. Biol. Chem., 2005)

Improving progressive alignment for phylogeny reconstruction using parsimonious guide-trees. - Usman Roshan; Dennis R. Livesay; Satish Chikkagoudar (BIBE, 2006)

Computational Grand Challenges in Assembling the Tree of Life: Problems and Solutions. - David A. Bader; Usman Roshan; Alexandros Stamatakis (Adv. Comput., 2006)

Probalign: multiple sequence alignment using partition function posterior probabilities. - Usman Roshan; Dennis R. Livesay (Bioinform., 2006)

PRec-I-DCM3: a parallel framework for fast and accurate large-scale phylogeny reconstruction. - Yuri Dotsenko; Cristian Coarfa; Luay Nakhleh; John M. Mellor-Crummey; Usman Roshan (Int. J. Bioinform. Res. Appl., 2006)

Assessing the ability of sequence-based methods to provide functional insight within membrane integral proteins: a case study analyzing the neurotransmitter/Na+ symporter family. - Dennis R. Livesay; Patrick D. Kidd; Sepehr Eskandari; Usman Roshan (BMC Bioinform., 2007)

eProbalign: generation and manipulation of multiple sequence alignments using partition function posterior probabilities. - Satish Chikkagoudar; Usman Roshan; Dennis R. Livesay (Nucleic Acids Res., 2007)

Searching for evolutionary distant RNA homologs within genomic sequences using partition function posterior probabilities. - Usman Roshan; Satish Chikkagoudar; Dennis R. Livesay (BMC Bioinform., 2008)

PLAST-ncRNA: Partition function Local Alignment Search Tool for non-coding RNA sequences. - Satish Chikkagoudar; Dennis R. Livesay; Usman Roshan (Nucleic Acids Res., 2010)

Weighted Maximum Variance Dimensionality Reduction. - Turki Turki; Usman Roshan (MCPR, 2014)

Top-k Parametrized Boost. - Turki Turki; Muhammad Ihsan; Nouf Turki; Jie Zhang 049; Usman Roshan; Zhi Wei 001 (MIKE, 2014)

Cross-validation and cross-study validation of chronic lymphocytic leukemia with exome sequences and machine learning. - Nihir Patel; Bharati Jhadav; Abdulrhman Aljouie; Usman Roshan (BIBM, 2015)

Prediction of Continuous Phenotypes in Mouse, Fly, and Rice Genome Wide Association Studies with Support Vector Regression SNPs and Ridge Regression Classifier. - Abdulrhman Aljouie; Usman Roshan (ICMLA, 2015)

Cross-validation and cross-study validation of chronic lymphocytic leukaemia with exome sequences and machine learning. - Abdulrhman Aljouie; Nihir Patel; Bharati Jadhav; Usman Roshan (Int. J. Data Min. Bioinform., 2016)

Cross-validation and cross-study validation of kidney cancer with machine learning and whole exome sequences from the National Cancer Institute. - Abdulrhman Aljouie; Nihir Patel; Usman Roshan (CIBCB, 2018)

Random depthwise signed convolutional neural networks. - Yunzhe Xue; Usman Roshan (CoRR, 2018)

Statistically Rigorous Testing of Clustering Implementations. - Xin Yin; Vincenzo Musco; Iulian Neamtiu; Usman Roshan (AITest, 2019)

Multi-path convolutional neural network for glioblastoma survival group prediction with point mutations and demographic features. - Abdulrhman Aljouie; Usman Roshan (BIBM, 2019)

Vessel lumen segmentation in internal carotid artery ultrasounds with deep convolutional neural networks. - Meiyan Xie; Yunzhu Li; Yunzhe Xue; Randy Shafritz; Saum A. Rahimi; Justin W. Ady; Usman W. Roshan (BIBM, 2019)

A Multi-path Decoder Network for Brain Tumor Segmentation. - Yunzhe Xue; Meiyan Xie; Fadi G. Farhat; Olga Boukrina; A. M. Barrett; Jeffrey R. Binder; Usman W. Roshan; William W. Graves (BrainLes@MICCAI (2), 2019)

Brain Tumor Classification with Tumor Segmentations and a Dual Path Residual Convolutional Neural Network from MRI and Pathology Images. - Yunzhe Xue; Yanan Yang; Fadi G. Farhat; Frank Y. Shih; Olga Boukrina; A. M. Barrett; Jeffrey R. Binder; William W. Graves; Usman W. Roshan (BrainLes@MICCAI (2), 2019)

Stochastic Coordinate Descent for 01 Loss and Its Sensitivity to Adversarial Attacks. - Meiyan Xie; Yunzhe Xue; Usman Roshan (ICMLA, 2019)

Exploring Classification, Clustering, and Its Limits in a Compressed Hidden Space of a Single Layer Neural Network with Random Weights. - Meiyan Xie; Usman Roshan (IWANN (1), 2019)

Image Classification and Retrieval with Random Depthwise Signed Convolutional Neural Networks. - Yunzhe Xue; Usman Roshan (IWANN (1), 2019)

A multi-path 2.5 dimensional convolutional neural network system for segmenting stroke lesions in brain MRI images. - Yunzhe Xue; Fadi G. Farhat; Olga Boukrina; A. M. Barrett; Jeffrey R. Binder; Usman W. Roshan; William W. Graves (CoRR, 2019)

A fully 3D multi-path convolutional neural network with feature fusion and feature weighting for automatic lesion identification in brain MRI images. - Yunzhe Xue; Meiyan Xie; Fadi G. Farhat; Olga Boukrina; A. M. Barrett; Jeffrey R. Binder; Usman W. Roshan; William W. Graves (CoRR, 2019)

Challenges in predicting glioma survival time in multi-modal deep networks. - Abdulrhman Aljouie; Yunzhe Xue; Meiyan Xie; Usman Roshan (BIBM, 2020)

Vessel lumen segmentation in carotid artery ultrasounds with the U-Net convolutional neural network. - Meiyan Xie; Yunzhi Li; Yunzhe Xue; Lauren Huntress; William Beckerman; Saum A. Rahimi; Justin W. Ady; Usman Roshan (BIBM, 2020)

Accurate and adversarially robust classification of medical images and ECG time-series with gradient-free trained sign activation neural networks. - Zhibo Yang; Yanan Yang; Yunzhe Xue; Frank Y. Shih; Justin W. Ady; Usman Roshan (BIBM, 2020)

Classification of Histopathology Images with Random Depthwise Convolutional Neural Networks. - Yanan Yang; Fadi G. Farhat; Yunzhe Xue; Frank Y. Shih; Usman Roshan (ICBRA, 2020)

Two-stage and dual-decoder convolutional U-Net ensembles for reliable vessel and plaque segmentation in carotid ultrasound images. - Meiyan Xie; Yunzhu Li; Yunzhe Xue; Lauren Huntress; William Beckerman; Saum A. Rahimi; Justin W. Ady; Usman W. Roshan (ICMLA, 2020)

Towards adversarial robustness with 01 loss neural networks. - Yunzhe Xue; Meiyan Xie; Usman Roshan (ICMLA, 2020)

On the transferability of adversarial examples between convex and 01 loss models. - Yunzhe Xue; Meiyan Xie; Usman Roshan (ICMLA, 2020)

Robust binary classification with the 01 loss. - Yunzhe Xue; Meiyan Xie; Usman Roshan (CoRR, 2020)

Defending against substitute model black box adversarial attacks with the 01 loss. - Yunzhe Xue; Meiyan Xie; Usman Roshan (CoRR, 2020)

High scoring segment selection for pairwise whole genome sequence alignment with the maximum scoring subsequence and GPUs. - Abdulrhman Aljouie; Ling Zhong; Usman Roshan (Int. J. Comput. Biol. Drug Des., 2020)

Defense Against Adversarial Attacks Based on Stochastic Descent Sign Activation Networks on Medical Images. - Yanan Yang; Frank Y. Shih; Usman Roshan (Int. J. Pattern Recognit. Artif. Intell., 2022)

An AI system for evaluating pass fail in fundamentals of laparoscopic surgery from live video in realtime with performative feedback. - Yunzhe Xue; Andrew Hu; Rohit Muralidhar; Justin W. Ady; Advaith Bongu; Usman Roshan (BIBM, 2023)

A Cascaded Neural Network System For Rating Student Performance In Surgical Knot Tying Simulation. - Yunzhe Xue; Olanrewaju Eletta; Justin W. Ady; Nell M. Patel; Advaith Bongu; Usman Roshan (ICHI, 2023)

Accuracy of white box and black box adversarial attacks on a sign activation 01 loss neural network ensemble. - Yunzhe Xue; Usman Roshan (Tiny Papers @ ICLR, 2023)

Accuracy of TextFooler black box adversarial attacks on 01 loss sign activation neural network ensemble. - Yunzhe Xue; Usman Roshan (CoRR, 2024)