Hamed Alhoori

Abdul Rahman Shaikh, Hamed Alhoori, Maoyuan Sun

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.

Murtuza Shahzad, Hamed Alhoori, Reva Freedman et al.

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).

Ibrahim Al Azher, Zhishuai Guo, Hamed Alhoori

Identifying and articulating limitations is essential for transparent and rigorous scientific research. However, zero-shot large language models (LLMs) approach often produce superficial or general limitation statements (e.g., dataset bias or generalizability). They usually repeat limitations reported by authors without looking at deeper methodological issues and contextual gaps. This problem is made worse because many authors disclose only partial or trivial limitations. We propose LimAgents, a multi-agent LLM framework for generating substantive limitations. LimAgents integrates OpenReview comments and author-stated limitations to provide stronger ground truth. It also uses cited and citing papers to capture broader contextual weaknesses. In this setup, different agents have specific roles as sequential role: some extract explicit limitations, others analyze methodological gaps, some simulate the viewpoint of a peer reviewer, and a citation agent places the work within the larger body of literature. A Judge agent refines their outputs, and a Master agent consolidates them into a clear set. This structure allows for systematic identification of explicit, implicit, peer review-focused, and literature-informed limitations. Moreover, traditional NLP metrics like BLEU, ROUGE, and cosine similarity rely heavily on n-gram or embedding overlap. They often overlook semantically similar limitations. To address this, we introduce a pointwise evaluation protocol that uses an LLM-as-a-Judge to measure coverage more accurately. Experiments show that LimAgents substantially improve performance. The RAG + multi-agent GPT-4o mini configuration achieves a +15.51% coverage gain over zero-shot baselines, while the Llama 3 8B multi-agent setup yields a +4.41% improvement.

Ashiqur Rahman, Ehsan Mohammadi, Hamed Alhoori

With the remarkable capability to reach the public instantly, social media has become integral in sharing scholarly articles to measure public response. Since spamming by bots on social media can steer the conversation and present a false public interest in given research, affecting policies impacting the public's lives in the real world, this topic warrants critical study and attention. We used the Altmetric dataset in combination with data collected through the Twitter Application Programming Interface (API) and the Botometer API. We combined the data into an extensive dataset with academic articles, several features from the article and a label indicating whether the article had excessive bot activity on Twitter or not. We analyzed the data to see the possibility of bot activity based on different characteristics of the article. We also trained machine-learning models using this dataset to identify possible bot activity in any given article. Our machine-learning models were capable of identifying possible bot activity in any academic article with an accuracy of 0.70. We also found that articles related to "Health and Human Science" are more prone to bot activity compared to other research areas. Without arguing the maliciousness of the bot activity, our work presents a tool to identify the presence of bot activity in the dissemination of an academic article and creates a baseline for future research in this direction.

Mosab Rezaei, Hamed Alhoori, Mona Rahimi

Frequent modifications of unit test cases are inevitable due to software's continuous underlying changes in source code, design, and requirements. Since manually maintaining software test suites is tedious, timely, and costly, automating the process of generation and maintenance of test units will significantly impact the effectiveness and efficiency of software testing processes. To this end, we propose an automated approach which exploits both structural and semantic properties of source code methods and test cases to recommend the most relevant and useful unit tests to the developers. The proposed approach initially trains a neural network to transform method-level source code, as well as unit tests, into distributed representations (embedded vectors) while preserving the importance of the structure in the code. Retrieving the semantic and structural properties of a given method, the approach computes cosine similarity between the method's embedding and the previously-embedded training instances. Further, according to the similarity scores between the embedding vectors, the model identifies the closest methods of embedding and the associated unit tests as the most similar recommendations. The results on the Methods2Test dataset showed that, while there is no guarantee to have similar relevant test cases for the group of similar methods, the proposed approach extracts the most similar existing test cases for a given method in the dataset, and evaluations show that recommended test cases decrease the developers' effort to generating expected test cases.

Ibrahim Al Azhar, Venkata Devesh Reddy, Hamed Alhoori et al.

The limitations sections of scientific articles play a crucial role in highlighting the boundaries and shortcomings of research, thereby guiding future studies and improving research methods. Analyzing these limitations benefits researchers, reviewers, funding agencies, and the broader academic community. We introduce LimTopic, a strategy where Topic generation in Limitation sections in scientific articles with Large Language Models (LLMs). Here, each topic contains the title and Topic Summary. This study focuses on effectively extracting and understanding these limitations through topic modeling and text summarization, utilizing the capabilities of LLMs. We extracted limitations from research articles and applied an LLM-based topic modeling integrated with the BERtopic approach to generate a title for each topic and Topic Sentences. To enhance comprehension and accessibility, we employed LLM-based text summarization to create concise and generalizable summaries for each topic Topic Sentences and produce a Topic Summary. Our experimentation involved prompt engineering, fine-tuning LLM and BERTopic, and integrating BERTopic with LLM to generate topics, titles, and a topic summary. We also experimented with various LLMs with BERTopic for topic modeling and various LLMs for text summarization tasks. Our results showed that the combination of BERTopic and GPT 4 performed the best in terms of silhouette and coherence scores in topic modeling, and the GPT4 summary outperformed other LLM tasks as a text summarizer.

Murtuza Shahzad, Joseph Wilson, Ibrahim Al Azher et al.

The increasing complexity and volume of software systems have heightened the importance of identifying and mitigating security vulnerabilities. The existing software vulnerability datasets frequently fall short in providing comprehensive, detailed code snippets explicitly linked to specific vulnerability descriptions, reducing their utility for advanced research and hindering efforts to develop a deeper understanding of security vulnerabilities. To address this challenge, we present a novel dataset that provides examples of vulnerable code snippets corresponding to Common Attack Pattern Enumerations and Classifications (CAPEC) and Common Weakness Enumeration (CWE) descriptions. By employing the capabilities of Generative Pre-trained Transformer (GPT) models, we have developed a robust methodology for generating these examples. Our approach utilizes GPT-4o, Llama and Claude models to generate code snippets that exhibit specific vulnerabilities as described in CAPEC and CWE documentation. This dataset not only enhances the understanding of security vulnerabilities in code but also serves as a valuable resource for training machine learning models focused on automatic vulnerability detection and remediation. Preliminary evaluations suggest that the dataset generated by Large Language Models demonstrates high accuracy and can serve as a reliable reference for vulnerability identification systems. We found consistent results across the three models, with 0.98 cosine similarity among codes. The final dataset comprises 615 CAPEC code snippets in three programming languages: Java, Python, and JavaScript, making it one of the most extensive and diverse resources in this domain.

Ibrahim Al Azher, Miftahul Jannat Mokarrama, Zhishuai Guo et al.

In scientific research, ``limitations'' refer to the shortcomings, constraints, or weaknesses of a study. A transparent reporting of such limitations can enhance the quality and reproducibility of research and improve public trust in science. However, authors often underreport limitations in their papers and rely on hedging strategies to meet editorial requirements at the expense of readers' clarity and confidence. This tendency, combined with the surge in scientific publications, has created a pressing need for automated approaches to extract and generate limitations from scholarly papers. To address this need, we present a full architecture for computational analysis of research limitations. Specifically, we (1) create a dataset of limitations from ACL, NeurIPS, and PeerJ papers by extracting them from the text and supplementing them with external reviews; (2) we propose methods to automatically generate limitations using a novel Retrieval Augmented Generation (RAG) technique; (3) we design a fine-grained evaluation framework for generated limitations, along with a meta-evaluation of these techniques.

Mosab Rezaei, Mina Rajaei Moghadam, Abdul Rahman Shaikh et al.

Recent advances in large language models have created new opportunities for stylometry, the study of writing styles and authorship. Two challenges, however, remain central: training generative models when no paired data exist, and evaluating stylistic text without relying only on human judgment. In this work, we present a framework for both generating and evaluating sentences in the style of 19th-century novelists. Large language models are fine-tuned with minimal, single-token prompts to produce text in the voices of authors such as Dickens, Austen, Twain, Alcott, and Melville. To assess these generative models, we employ a transformer-based detector trained on authentic sentences, using it both as a classifier and as a tool for stylistic explanation. We complement this with syntactic comparisons and explainable AI methods, including attention-based and gradient-based analyses, to identify the linguistic cues that drive stylistic imitation. Our findings show that the generated text reflects the authors' distinctive patterns and that AI-based evaluation offers a reliable alternative to human assessment. All artifacts of this work are published online.

Ashiqur Rahman, Hamed Alhoori

The integration of machine learning (ML) is critical for industrial competitiveness, yet its adoption is frequently stalled by the prohibitive costs and operational disruptions of upgrading legacy systems. The financial and logistical overhead required to support the full ML lifecycle presents a formidable barrier to widespread implementation, particularly for small and medium-sized enterprises. This paper introduces a pragmatic, API-based framework designed to overcome these challenges by strategically decoupling the ML model lifecycle from the production environment. Our solution delivers the analytical power of ML to domain experts through a lightweight, browser-based interface, eliminating the need for local hardware upgrades and ensuring model maintenance can occur with zero production downtime. This human-in-the-loop approach empowers experts with interactive control over model parameters, fostering trust and facilitating seamless integration into existing workflows. By mitigating the primary financial and operational risks, this framework offers a scalable and accessible pathway to enhance production quality and safety, thereby strengthening the competitive advantage of the manufacturing sector.

Ibrahim Al Azher, Miftahul Jannat Mokarrama, Zhishuai Guo et al.

The Future Work section of a scientific article outlines potential research directions by identifying gaps and limitations of a current study. This section serves as a valuable resource for early-career researchers seeking unexplored areas and experienced researchers looking for new projects or collaborations. In this study, we generate future work suggestions from a scientific article. To enrich the generation process with broader insights and reduce the chance of missing important research directions, we use context from related papers using RAG. We experimented with various Large Language Models (LLMs) integrated into Retrieval-Augmented Generation (RAG). We incorporate an LLM feedback mechanism to enhance the quality of the generated content and introduce an LLM-as-a-judge framework for robust evaluation, assessing key aspects such as novelty, hallucination, and feasibility. Our results demonstrate that the RAG-based approach using GPT-4o mini, combined with an LLM feedback mechanism, outperforms other methods based on both qualitative and quantitative evaluations. Moreover, we conduct a human evaluation to assess the LLM as an extractor, generator, and feedback provider.

Miftahul Jannat Mokarrama, Hamed Alhoori

In recent years, there has been a growing concern and emphasis on conducting research beyond academic or scientific research communities, benefiting society at large. A well-known approach to measuring the impact of research on society is enumerating its policy citation(s). Despite the importance of research in informing policy, there is no concrete evidence to suggest the research's relevance in cited policy documents. This is concerning because it may increase the possibility of evidence used in policy being manipulated by individual, social, or political biases that may lead to inappropriate, fragmented, or archaic research evidence in policy. Therefore, it is crucial to identify the degree of relevance between research articles and citing policy documents. In this paper, we examined the scale of contextual relevance of youth-focused research in the referenced US policy documents using natural language processing techniques, state-of-the-art pre-trained Large Language Models (LLMs), and statistical analysis. Our experiments and analysis concluded that youth-related research articles that get US policy citations are mostly relevant to the citing policy documents.

Ashiqur Rahman, Venkata Devesh Reddy Seethi, Austin Yunker et al.

Ultrasonic testing is a common Non-Destructive Inspection (NDI) method used in aerospace manufacturing. However, the complexity and size of the ultrasonic scans make it challenging to identify defects through visual inspection or machine learning models. Using computer vision techniques to identify defects from ultrasonic scans is an evolving research area. In this study, we used instance segmentation to identify the presence of defects in the ultrasonic scan images of composite panels that are representative of real components manufactured in aerospace. We used two models based on Mask-RCNN (Detectron 2) and YOLO 11 respectively. Additionally, we implemented a simple statistical pre-processing technique that reduces the burden of requiring custom-tailored pre-processing techniques. Our study demonstrates the feasibility and effectiveness of using instance segmentation in the NDI pipeline by significantly reducing data pre-processing time, inspection time, and overall costs.

Ashiqur Rahman, Ehsan Mohammadi, Hamed Alhoori

The COVID-19 pandemic exposed significant weaknesses in the healthcare information system. The overwhelming volume of misinformation on social media and other socioeconomic factors created extraordinary challenges to motivate people to take proper precautions and get vaccinated. In this context, our work explored a novel direction by analyzing an extensive dataset collected over two years, identifying the topics de/motivating the public about COVID-19 vaccination. We analyzed these topics based on time, geographic location, and political orientation. We noticed that while the motivating topics remain the same over time and geographic location, the demotivating topics change rapidly. We also identified that intrinsic motivation, rather than external mandate, is more advantageous to inspire the public. This study addresses scientific communication and public motivation in social media. It can help public health officials, policymakers, and social media platforms develop more effective messaging strategies to cut through the noise of misinformation and educate the public about scientific findings.

Murtuza Shahzad, Hamed Alhoori

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.

Venkata Devesh Reddy Seethi, Zane LaCasse, Prajkta Chivte et al.

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

Maoyuan Sun, Abdul Rahman Shaikh, Hamed Alhoori et al.

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.

Akhil Pandey Akella, Hamed Alhoori, Pavan Ravikanth Kondamudi et al.

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.

Wesam Alruwaili, Bradley Protano, Tejasvi Sirigiriraju et al.

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%).

Abdul Rahman Shaikh, Hamed Alhoori

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.

Cole Freeman, Mrinal Kanti Roy, Michele Fattoruso et al.

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.

Hamed Alhoori, Mohammed Samaka, Richard Furuta et al.

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.