arXiv subjects

Hamed Alhoori

Publications and source records attributed to Hamed Alhoori.

36 records · Page 2Linked to original sources

arXiv2023

An Explainable-AI approach for Diagnosis of COVID-19 using MALDI-ToF Mass Spectrometry

The severe acute respiratory syndrome coronavirus type-2 (SARS-CoV-2) caused a global pandemic and immensely affected the global economy. Accurate, cost-effective, and quick tests have proven substantial in identifying infected people and mitigating the spread. Recently, multiple alternative platforms for testing coronavirus disease 2019 (COVID-19) have been published that show high agreement with current gold standard real-time polymerase chain reaction (RT-PCR) results. These new methods do away with nasopharyngeal (NP) swabs, eliminate the need for complicated reagents, and reduce the burden on RT-PCR test reagent supply. In the present work, we have designed an artificial intelligence-based (AI) testing method to provide confidence in the results. Current AI applications for COVID-19 studies often lack a biological foundation in the decision-making process, and our AI approach is one of the earliest to leverage explainable AI (X-AI) algorithms for COVID-19 diagnosis using mass spectrometry. Here, we have employed X-AI to explain the decision-making process on a local (per-sample) and global (all samples) basis underscored by biologically relevant features. We evaluated our technique with data extracted from human gargle samples and achieved a testing accuracy of 94.12%. Such techniques would strengthen the relationship between AI and clinical diagnostics by providing biomedical researchers and healthcare workers with trustworthy and, most importantly, explainable test results

cs.LG↗

arXiv2023

Reproducibility Signals in Science: A preliminary analysis

Reproducibility is an important feature of science; experiments are retested, and analyses are repeated. Trust in the findings increases when consistent results are achieved. Despite the importance of reproducibility, significant work is often involved in these efforts, and some published findings may not be reproducible due to oversights or errors. In this paper, we examine a myriad of features in scholarly articles published in computer science conferences and journals and test how they correlate with reproducibility. We collected data from three different sources that labeled publications as either reproducible or irreproducible and employed statistical significance tests to identify features of those publications that hold clues about reproducibility. We found the readability of the scholarly article and accessibility of the software artifacts through hyperlinks to be strong signals noticeable amongst reproducible scholarly articles.

cs.DL↗

arXiv2022

Quantifying the Online Long-Term Interest in Research

Research articles are being shared in increasing numbers on multiple online platforms. Although the scholarly impact of these articles has been widely studied, the online interest determined by how long the research articles are shared online remains unclear. Being cognizant of how long a research article is mentioned online could be valuable information to the researchers. In this paper, we analyzed multiple social media platforms on which users share and/or discuss scholarly articles. We built three clusters for papers, based on the number of yearly online mentions having publication dates ranging from the year 1920 to 2016. Using the online social media metrics for each of these three clusters, we built machine learning models to predict the long-term online interest in research articles. We addressed the prediction task with two different approaches: regression and classification. For the regression approach, the Multi-Layer Perceptron model performed best, and for the classification approach, the tree-based models performed better than other models. We found that old articles are most evident in the contexts of economics and industry (i.e., patents). In contrast, recently published articles are most evident in research platforms (i.e., Mendeley) followed by social media platforms (i.e., Twitter).

cs.DL↗

arXiv2022

Public Reaction to Scientific Research via Twitter Sentiment Prediction

Social media users share their ideas, thoughts, and emotions with other users. However, it is not clear how online users would respond to new research outcomes. This study aims to predict the nature of the emotions expressed by Twitter users toward scientific publications. Additionally, we investigate what features of the research articles help in such prediction. Identifying the sentiments of research articles on social media will help scientists gauge a new societal impact of their research articles.

cs.IR↗

arXiv2022

YouTube and Science: Models for Research Impact

Video communication has been rapidly increasing over the past decade, with YouTube providing a medium where users can post, discover, share, and react to videos. There has also been an increase in the number of videos citing research articles, especially since it has become relatively commonplace for academic conferences to require video submissions. However, the relationship between research articles and YouTube videos is not clear, and the purpose of the present paper is to address this issue. We created new datasets using YouTube videos and mentions of research articles on various online platforms. We found that most of the articles cited in the videos are related to medicine and biochemistry. We analyzed these datasets through statistical techniques and visualization, and built machine learning models to predict (1) whether a research article is cited in videos, (2) whether a research article cited in a video achieves a level of popularity, and (3) whether a video citing a research article becomes popular. The best models achieved F1 scores between 80% and 94%. According to our results, research articles mentioned in more tweets and news coverage have a higher chance of receiving video citations. We also found that video views are important for predicting citations and increasing research articles' popularity and public engagement with science.

cs.DL↗

arXiv2022

Toward Systematic Design Considerations of Organizing Multiple Views

Multiple-view visualization (MV) has been used for visual analytics in various fields (e.g., bioinformatics, cybersecurity, and intelligence analysis). Because each view encodes data from a particular perspective, analysts often use a set of views laid out in 2D space to link and synthesize information. The difficulty of this process is impacted by the spatial organization of these views. For instance, connecting information from views far from each other can be more challenging than neighboring ones. However, most visual analysis tools currently either fix the positions of the views or completely delegate this organization of views to users (who must manually drag and move views). This either limits user involvement in managing the layout of MV or is overly flexible without much guidance. Then, a key design challenge in MV layout is determining the factors in a spatial organization that impact understanding. To address this, we review a set of MV-based systems and identify considerations for MV layout rooted in two key concerns: perception, which considers how users perceive view relationships, and content, which considers the relationships in the data. We show how these allow us to study and analyze the design of MV layout systematically.

cs.HC↗

arXiv2021

SightBi: Exploring Cross-View Data Relationships with Biclusters

Multiple-view visualization (MV) has been heavily used in visual analysis tools for sensemaking of data in various domains (e.g., bioinformatics, cybersecurity and text analytics). One common task of visual analysis with multiple views is to relate data across different views. For example, to identify threats, an intelligence analyst needs to link people from a social network graph with locations on a crime-map, and then search for and read relevant documents. Currently, exploring cross-view data relationships heavily relies on view-coordination techniques (e.g., brushing and linking), which may require significant user effort on many trial-and-error attempts, such as repetitiously selecting elements in one view, and then observing and following elements highlighted in other views. To address this, we present SightBi, a visual analytics approach for supporting cross-view data relationship explorations. We discuss the design rationale of SightBi in detail, with identified user tasks regarding the use of cross-view data relationships. SightBi formalizes cross-view data relationships as biclusters, computes them from a dataset, and uses a bi-context design that highlights creating stand-alone relationship-views. This helps preserve existing views and offers an overview of cross-view data relationships to guide user exploration. Moreover, SightBi allows users to interactively manage the layout of multiple views by using newly created relationship-views. With a usage scenario, we demonstrate the usefulness of SightBi for sensemaking of cross-view data relationships.

cs.HC↗

arXiv2020

Early Indicators of Scientific Impact: Predicting Citations with Altmetrics

Identifying important scholarly literature at an early stage is vital to the academic research community and other stakeholders such as technology companies and government bodies. Due to the sheer amount of research published and the growth of ever-changing interdisciplinary areas, researchers need an efficient way to identify important scholarly work. The number of citations a given research publication has accrued has been used for this purpose, but these take time to occur and longer to accumulate. In this article, we use altmetrics to predict the short-term and long-term citations that a scholarly publication could receive. We build various classification and regression models and evaluate their performance, finding neural networks and ensemble models to perform best for these tasks. We also find that Mendeley readership is the most important factor in predicting the early citations, followed by other factors such as the academic status of the readers (e.g., student, postdoc, professor), followers on Twitter, online post length, author count, and the number of mentions on Twitter, Wikipedia, and across different countries.

cs.DL↗

arXiv2020

Measuring the Diversity of Facebook Reactions to Research

Online and in the real world, communities are bonded together by emotional consensus around core issues. Emotional responses to scientific findings often play a pivotal role in these core issues. When there is too much diversity of opinion on topics of science, emotions flare up and give rise to conflict. This conflict threatens positive outcomes for research. Emotions have the power to shape how people process new information. They can color the public's understanding of science, motivate policy positions, even change lives. And yet little work has been done to evaluate the public's emotional response to science using quantitative methods. In this paper, we use a dataset of responses to scholarly articles on Facebook to analyze the dynamics of emotional valence, intensity, and diversity. We present a novel way of weighting click-based reactions that increases their comprehensibility, and use these weighted reactions to develop new metrics of aggregate emotional responses. We use our metrics along with LDA topic models and statistical testing to investigate how users' emotional responses differ from one scientific topic to another. We find that research articles related to gender, genetics, or agricultural/environmental sciences elicit significantly different emotional responses from users than other research topics. We also find that there is generally a positive response to scientific research on Facebook, and that articles generating a positive emotional response are more likely to be widely shared---a conclusion that contradicts previous studies of other social media platforms.

cs.SI↗

arXiv2019

Using Arabic Tweets to Understand Drug Selling Behaviors

Twitter is a popular platform for e-commerce in the Arab region including the sale of illegal goods and services. Social media platforms present multiple opportunities to mine information about behaviors pertaining to both illicit and pharmaceutical drugs and likewise to legal prescription drugs sold without a prescription, i.e., illegally. Recognized as a public health risk, the sale and use of illegal drugs, counterfeit versions of legal drugs, and legal drugs sold without a prescription constitute a widespread problem that is reflected in and facilitated by social media. Twitter provides a crucial resource for monitoring legal and illegal drug sales in order to support the larger goal of finding ways to protect patient safety. We collected our dataset using Arabic keywords. We then categorized the data using four machine learning classifiers. Based on a comparison of the respective results, we assessed the accuracy of each classifier in predicting two important considerations in analysing the extent to which drugs are available on social media: references to drugs for sale and the legality/illegality of the drugs thus advertised. For predicting tweets selling drugs, Support Vector Machine, yielded the highest accuracy rate (96%), whereas for predicting the legality of the advertised drugs, the Naive Bayes, classifier yielded the highest accuracy rate (85%).

cs.CY↗

arXiv2019

Predicting Patent Citations to measure Economic Impact of Scholarly Research

A crucial goal of funding research and development has always been to advance economic development. On this basis, a consider-able body of research undertaken with the purpose of determining what exactly constitutes economic impact and how to accurately measure that impact has been published. Numerous indicators have been used to measure economic impact, although no single indicator has been widely adapted. Based on patent data collected from Altmetric we predict patent citations through various social media features using several classification models. Patents citing a research paper implies the potential it has for direct application inits field. These predictions can be utilized by researchers in deter-mining the practical applications for their work when applying for patents.

cs.DL↗

arXiv2019

Shared Feelings: Understanding Facebook Reactions to Scholarly Articles

Research on social-media platforms has tended to rely on textual analysis to perform research tasks. While text-based approaches have significantly increased our understanding of online behavior and social dynamics, they overlook features on these platforms that have grown in prominence in the past few years: click-based responses to content. In this paper, we present a new dataset of Facebook Reactions to scholarly content. We give an overview of its structure, analyze some of the statistical trends in the data, and use it to train and test two supervised learning algorithms. Our preliminary tests suggest the presence of stratification in the number of users following pages, divisions that seem to fall in line with distinctions in the subject matter of those pages.

cs.SI↗

arXiv2018

Anatomy of Scholarly Information Behavior Patterns in the Wake of Academic Social Media Platforms

As more scholarly content is born digital or converted to a digital format, digital libraries are becoming increasingly vital to researchers seeking to leverage scholarly big data for scientific discovery. Although scholarly products are available in abundance-especially in environments created by the advent of social networking services-little is known about international scholarly information needs, information-seeking behavior, or information use. The purpose of this paper is to address these gaps via an in-depth analysis of the information needs and information-seeking behavior of researchers, both students and faculty, at two universities, one in the U.S. and the other in Qatar. Based on this analysis, the study identifies and describes new behavior patterns on the part of researchers as they engage in the information-seeking process. The analysis reveals that the use of academic social networks has notable effects on various scholarly activities. Further, this study identifies differences between students and faculty members in regard to their use of academic social networks, and it identifies differences between researchers according to discipline. Although the researchers who participated in the present study represent a range of disciplinary and cultural backgrounds, the study reports a number of similarities in terms of the researchers' scholarly activities.

cs.DL↗

arXiv2018

What Makes A Research Article Newsworthy?

There has been tremendous growth in the amount of scientific literature being published every year. Yet, very little of it receives press coverage. Mentions by news outlets often establish the relevance the research has to society in general. In the present study, we focused on better understanding the factors that contribute to a research article's newsworthiness. We have built three classifiers to predict the likelihood of research article receiving online press coverage, based on features that quantify the attention it has received on various online platforms. The Random Forest classifier performed best with an accuracy rate of 0.92.

cs.CY↗

arXiv2017

Recommendation of Scholarly Venues Based on Dynamic User Interests

The ever-growing number of venues publishing academic work makes it difficult for researchers to identify venues that publish data and research most in line with their scholarly interests. A solution is needed, therefore, whereby researchers can identify information dissemination pathways in order to both access and contribute to an existing body of knowledge. In this study, we present a system to recommend scholarly venues rated in terms of relevance to a given researcher's current scholarly pursuits and interests. We collected our data from an academic social network and modeled researchers' scholarly reading behavior in order to propose a new and adaptive implicit rating technique for venues. We present a way to recommend relevant, specialized scholarly venues using these implicit ratings that can provide quick results, even for new researchers without a publication history and for emerging scholarly venues that do not yet have an impact factor. We performed a large-scale experiment with real data to evaluate the current scholarly recommendation system and showed that our proposed system achieves better results than the baseline. The results provide important up-to-the-minute signals that compared with post-publication usage-based metrics represent a closer reflection of a researcher's interests.

cs.SI↗

arXiv2017

Exploring Features for Predicting Policy Citations

In this study we performed an initial investigation and evaluation of altmetrics and their relationship with public policy citation of research papers. We examined methods for using altmetrics and other data to predict whether a research paper is cited in public policy and applied receiver operating characteristic curve on various feature groups in order to evaluate their potential usefulness. From the methods we tested, classifying based on tweet count provided the best results, achieving an area under the ROC curve of 0.91.

cs.DL↗

arXiv2017

Predicting Research that will be Cited in Policy Documents

Scientific publications and other genres of research output are increasingly being cited in policy documents. Citations in documents of this nature could be considered a critical indicator of the significance and societal impact of the research output. In this study, we built classification models that predict whether a particular research work is likely to be cited in a public policy document based on the attention it received online, primarily on social media platforms. We evaluated the classifiers based on their accuracy, precision, and recall values. We found that Random Forest and Multinomial Naive Bayes classifiers performed better overall.

cs.DL↗

arXiv2017

Pokémon Go: Impact on Yelp Restaurant Reviews

Pokémon Go, the popular Augmented Reality based mobile application, launched in July of 2016. The game's meteoric rise in usage since that time has had an impact on not just the mobile gaming industry, but also the physical activity of players, where they travel, where they spend their money, and possibly how they interact with other social media applications. In this paper, we studied the impact of Pokémon Go on Yelp reviews. For restaurants near PokéStops, we found a slight drop in the number of online reviews.

cs.CY↗