Search Results - "Roshan, Usman"

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

“…•Time and effort for hand-segmenting lesions bottlenecks brain lesion-deficit studies.•We provide a fully-automated tool for stroke brain lesion…”
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Probalign: multiple sequence alignment using partition function posterior probabilities by Roshan, Usman, Livesay, Dennis R.

“…Motivation: The maximum expected accuracy optimization criterion for multiple sequence alignment uses pairwise posterior probabilities of residues to align…”
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Chi8: a GPU program for detecting significant interacting SNPs with the Chi-square 8-df test by Al-jouie, Abdulrhman, Esfandiari, Mohammadreza, Ramakrishnan, Srividya, Roshan, Usman

“…Determining interacting SNPs in genome-wide association studies is computationally expensive yet of considerable interest in genomics. We present a program…”
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Diametrical clustering for identifying anti-correlated gene clusters by Dhillon, Inderjit S., Marcotte, Edward M., Roshan, Usman

“…Motivation: Clustering genes based upon their expression patterns allows us to predict gene function. Most existing clustering algorithms cluster genes…”
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Searching for evolutionary distant RNA homologs within genomic sequences using partition function posterior probabilities by Roshan, Usman, Chikkagoudar, Satish, Livesay, Dennis R

“…Identification of RNA homologs within genomic stretches is difficult when pairwise sequence identity is low or unalignable flanking residues are present. In…”
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Assessing the ability of sequence-based methods to provide functional insight within membrane integral proteins: a case study analyzing the neurotransmitter/Na+ symporter family by Livesay, Dennis R, Kidd, Patrick D, Eskandari, Sepehr, Roshan, Usman

“…Efforts to predict functional sites from globular proteins is increasingly common; however, the most successful of these methods generally require structural…”
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A Cascaded Neural Network System For Rating Student Performance In Surgical Knot Tying Simulation by Xue, Yunzhe, Eletta, Olanrewaju, Ady, Justin W., Patel, Nell M., Bongu, Advaith, Roshan, Usman

“…As part of their training all medical students and residents have to pass basic surgical tasks such as knot tying, needle-passing, and suturing. Their…”
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Two-stage and dual-decoder convolutional U-Net ensembles for reliable vessel and plaque segmentation in carotid ultrasound images by Xie, Meiyan, Li, Yunzhu, Xue, Yunzhe, Huntress, Lauren, Beckerman, William, Rahimi, Saum A., Ady, Justin W., Roshan, Usman W.

“…Carotid ultrasound is a screening modality used by physicians to direct treatment in the prevention of ischemic stroke in high-risk patients. It is a time…”
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Vessel lumen segmentation in internal carotid artery ultrasounds with deep convolutional neural networks by Xie, Meiyan, Li, Yunzhu, Xue, Yunzhe, Shafritz, Randy, Rahimi, Saum A., Ady, Justin W., Roshan, Usman W.

“…Carotid ultrasound is a screening modality used by physicians to direct treatment in the prevention of ischemic stroke in high-risk patients. It is a time…”
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Designing fast converging phylogenetic methods by Nakhleh, Luay, Roshan, Usman, St. John, Katherine, Sun, Jerry, Warnow, Tandy

“…Absolute fast converging phylogenetic reconstruction methods are provably guaranteed to recover the true tree with high probability from sequences that grow…”
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MaxSSmap: a GPU program for mapping divergent short reads to genomes with the maximum scoring subsequence by Turki, Turki, Roshan, Usman

“…Programs based on hash tables and Burrows-Wheeler are very fast for mapping short reads to genomes but have low accuracy in the presence of mismatches and…”
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Reconstruction of large phylogenetic trees: A parallel approach by Du, Zhihua, Lin, Feng, Roshan, Usman W.

“…Reconstruction of phylogenetic trees for very large datasets is a known example of a computationally hard problem. In this paper, we present a parallel…”
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MaxSSmap: A GPU program for mapping divergent short reads to genomes with the maximum scoring subsequence by Turki, Turki, Roshan, Usman

“…Programs based on hash tables and Burrows-Wheeler are very fast for mapping short reads to genomes but have low accuracy in the presence of mismatches and…”
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Ranking causal variants and associated regions in genome-wide association studies by the support vector machine and random forest by Roshan, Usman, Chikkagoudar, Satish, Wei, Zhi, Wang, Kai, Hakonarson, Hakon

“…We study the number of causal variants and associated regions identified by top SNPs in rankings given by the popular 1 df chi-squared statistic, support…”
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An Ensemble-Based Confidence Score to Increase Accuracy of Carotid Ultrasound Vessel Lumen Segmentation by Convolutional Neural Networks by Huntress, Lauren A., Xie, Meiyan, Huang, Shih-Yau G., Beckerman, William, Rahimi, Saum, Roshan, Usman W., Ady, Justin

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Multiple sequence alignment using Probcons and Probalign by Roshan, Usman

“…Sequence alignment remains a fundamental task in bioinformatics. The literature contains programs that employ a host of exact and heuristic strategies…”
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Accuracy of TextFooler black box adversarial attacks on 01 loss sign activation neural network ensemble by Xue, Yunzhe, Roshan, Usman

“…Recent work has shown the defense of 01 loss sign activation neural networks against image classification adversarial attacks. A public challenge to attack the…”
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Rec-I-DCM3: a fast algorithmic technique for reconstructing large phylogenetic trees by Roshan, Usman W, Moret, Bernard M, Warnow, Tandy, Williams, Tiffani L

“…Phylogenetic trees are commonly reconstructed based on hard optimization problems such as maximum parsimony (MP) and maximum likelihood (ML). Conventional MP…”
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PLAST-ncRNA: Partition function Local Alignment Search Tool for non-coding RNA sequences by Chikkagoudar, Satish, Livesay, Dennis R, Roshan, Usman

“…Alignment-based programs are valuable tools for finding potential homologs in genome sequences. Previously, it has been shown that partition function posterior…”
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Multi-path convolutional neural network for glioblastoma survival group prediction with point mutations and demographic features by Aljouie, Abdulrhman, Roshan, Usman

“…Glioblastoma multiforme (GBM) is the most common and aggressive brain cancer with a median survival rate of 15 months. It is well-established that age is a…”
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