Physical Sciences and Mathematics Commons^™

A Survey Of Matrix Completion Methods For Recommendation Systems, Andy Ramlatchan, Mengyun Yang, Quan Liu, Min Li, Jianxin Wang, Yaohang Li

Computer Science Faculty Publications

In recent years, the recommendation systems have become increasingly popular and have been used in a broad variety of applications. Here, we investigate the matrix completion techniques for the recommendation systems that are based on collaborative filtering. The collaborative filtering problem can be viewed as predicting the favorability of a user with respect to new items of commodities. When a rating matrix is constructed with users as rows, items as columns, and entries as ratings, the collaborative filtering problem can then be modeled as a matrix completion problem by filling out the unknown elements in the rating matrix. This article …

Tracing Actin Filament Bundles In Three-Dimensional Electron Tomography Density Maps Of Hair Cell Stereocilia, Salim Sazzed, Junha Song, Julio Kovacs, Willi Wriggers, Manfred Auer, Jing He

Computer Science Faculty Publications

Cryo-electron tomography (cryo-ET) is a powerful method of visualizing the three-dimensional organization of supramolecular complexes, such as the cytoskeleton, in their native cell and tissue contexts. Due to its minimal electron dose and reconstruction artifacts arising from the missing wedge during data collection, cryo-ET typically results in noisy density maps that display anisotropic XY versus Z resolution. Molecular crowding further exacerbates the challenge of automatically detecting supramolecular complexes, such as the actin bundle in hair cell stereocilia. Stereocilia are pivotal to the mechanoelectrical transduction process in inner ear sensory epithelial hair cells. Given the complexity and dense arrangement of actin …

Prediction Of Lncrna-Disease Associations Based On Inductive Matrix Completion, Chengqian Lu, Mengyun Yang, Feng Luo, Fang-Xiang Wu, Min Li, Yi Pan, Yaohang Li, Jianxin Wang

Computer Science Faculty Publications

Motivation: Accumulating evidences indicate that long non-coding RNAs (lncRNAs) play pivotal roles in various biological processes. Mutations and dysregulations of lncRNAs are implicated in miscellaneous human diseases. Predicting lncRNA–disease associations is beneficial to disease diagnosis as well as treatment. Although many computational methods have been developed, precisely identifying lncRNA–disease associations, especially for novel lncRNAs, remains challenging.

Results: In this study, we propose a method (named SIMCLDA) for predicting potential lncRNA– disease associations based on inductive matrix completion. We compute Gaussian interaction profile kernel of lncRNAs from known lncRNA–disease interactions and functional similarity of diseases based on disease–gene and gene–gene onotology …

Unobtrusive And Extensible Archival Replay Banners Using Custom Elements, Sawood Alam, Mat Kelly, Michele C. Weigle, Michael L. Nelson

Computer Science Faculty Publications

We compare and contrast three different ways to implement an archival replay banner. We propose an implementation that utilizes Custom Elements and adds some unique behaviors, not common in existing archival replay systems, to enhance the user experience. Our approach has a minimal user interface footprint and resource overhead while still providing rich interactivity and extended on-demand provenance information about the archived resources.

Quantification Of Twist From The Central Lines Of Β-Strands, Tunazzina Islam, Michael Poteat, Jing He

Computer Science Faculty Publications

Since the discovery of right-handed twist of a β-strand, many studies have been conducted to understand the twist. Given the atomic structure of a protein, twist angles have been defined using atomic positions of the backbone. However, limited study is available to characterize twist when the atomic positions are not available, but the central lines of β-strands are. Recent studies in cryoelectron microscopy show that it is possible to predict the central lines of β-strands from a medium-resolution density map. Accurate measurement of twist angles is important in identification of β-strands from such density maps. We propose an effective method …

Efficient Randomized Algorithms For The Fixed Precision Low Rank Matrix Approximation, Wenjian Yu, Yu Gu, Yaohang Li

Computer Science Faculty Publications

Randomized algorithms for low-rank matrix approximation are investigated, with the emphasis on the fixed-precision problem and computational efficiency for handling large matrices. The algorithms are based on the so-called QB factorization, where Q is an orthonormal matrix. First, a mechanism for calculating the approximation error in the Frobenius norm is proposed, which enables efficient adaptive rank determination for a large and/or sparse matrix. It can be combined with any QB-form factorization algorithm in which B's rows are incrementally generated. Based on the blocked randQB algorithm by Martinsson and Voronin, this results in an algorithm called randQB_EI. Then, we further revise …

205.3 The Many Shapes Of Archive-It, Shawn Jones, Michael L. Nelson, Alexander Nwala, Michele C. Weigle

Computer Science Faculty Publications

Web archives, a key area of digital preservation, meet the needs of journalists, social scientists, historians, and government organizations. The use cases for these groups often require that they guide the archiving process themselves, selecting their own original resources, or seeds, and creating their own web archive collections. We focus on the collections within Archive-It, a subscription service started by the Internet Archive in 2005 for the purpose of allowing organizations to create their own collections of archived web pages, or mementos. Understanding these collections could be done via their user-supplied metadata or via text analysis, but the metadata is …

A Survey Of Archival Replay Banners, Sawood Alam, Mat Kelly, Michele C. Weigle, Michael L. Nelson

Computer Science Faculty Publications

We surveyed various archival systems to compare and contrast different techniques used to implement an archival replay banner. We found that inline plain HTML injection is the most common approach, but prone to style conflicts. Iframe-based banners are also very common and while they do not have style conflicts, they suffer from screen real estate wastage and limited design choices. Custom Elements-based banners are promising, but due to being a new web standard, these are not yet widely deployed.

Swimming In A Sea Of Javascript Or: How I Learned To Stop Worrying And Love High-Fidelity Replay, John A. Berlin, Michael L. Nelson, Michele C. Weigle

Computer Science Faculty Publications

[First paragraph] Preserving and replaying modern web pages in high-fidelity has become an increasingly difficult task due to the increased usage of JavaScript. Reliance on server-side rewriting alone results in live-leakage and or the inability to replay a page due to the preserved JavaScript performing an action not permissible from the archive. The current state-of-the-art high fidelity archival preservation and replay solutions rely on handcrafted client-side URL rewriting libraries specifically tailored for the archive, namely Webrecoder's and Pywb's wombat.js [12]. Web archives not utilizing client-side rewriting rely on server-side rewriting that misses URLs used in a manner not accounted for …

It Is Hard To Compute Fixity On Archived Web Pages, Mohamed Aturban, Michael L. Nelson, Michele C. Weigle

Computer Science Faculty Publications

[Introduction] Checking fixity in web archives is performed to ensure archived resources, or mementos (denoted by URI-M) have remained unaltered since when they were captured. The final report of the PREMIS Working Group [2] defines information used for fixity as "information used to verify whether an object has been altered in an undocumented or unauthorized way." The common technique for checking fixity is to generate a current hash value (i.e., a message digest or a checksum) for a file using a cryptographic hash function (e.g., SHA-256) and compare it to the hash value generated originally. If they have different hash …

Client-Assisted Memento Aggregation Using The Prefer Header, Mat Kelly, Sawood Alam, Michael L. Nelson, Michele C. Weigle

Computer Science Faculty Publications

[First paragraph] Preservation of the Web ensures that future generations have a picture of how the web was. Web archives like Internet Archive's Wayback Machine, WebCite, and archive.is allow individuals to submit URIs to be archived, but the captures they preserve then reside at the archives. Traversing these captures in time as preserved by multiple archive sources (using Memento [8]) provides a more comprehensive picture of the past Web than relying on a single archive. Some content on the Web, such as content behind authentication, may be unsuitable or inaccessible for preservation by these organizations. Furthermore, this content may be …