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Researcher profile

Basem Suleiman

Basem Suleiman contributes to research discovery and scholarly infrastructure.

ResearcherAffiliation not importedOpen to collaborate
Artificial IntelligenceMachine LearningComputation and LanguageQuantitative MethodsSoftware Engineering

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Published work

5 published item(s)

preprint2026arXiv

Benchmarking Preprocessing and Integration Methods in Single-Cell Genomics

Single-cell data analysis has the potential to revolutionize personalized medicine by characterizing disease-associated molecular changes at the single-cell level. Advanced single-cell multimodal assays can now simultaneously measure various molecules (e.g., DNA, RNA, Protein) across hundreds of thousands of individual cells, providing a comprehensive molecular readout. A significant analytical challenge is integrating single-cell measurements across different modalities. Various methods have been developed to address this challenge, but there has been no systematic evaluation of these techniques with different preprocessing strategies. This study examines a general pipeline for single-cell data analysis, which includes normalization, data integration, and dimensionality reduction. The performance of different algorithm combinations often depends on the dataset sizes and characteristics. We evaluate six datasets across diverse modalities, tissues, and organisms using three metrics: Silhouette Coefficient Score, Adjusted Rand Index, and Calinski-Harabasz Index. Our experiments involve combinations of seven normalization methods, four dimensional reduction methods, and five integration methods. The results show that Seurat and Harmony excel in data integration, with Harmony being more time-efficient, especially for large datasets. UMAP is the most compatible dimensionality reduction method with the integration techniques, and the choice of normalization method varies depending on the integration method used.

0 citations0 reviewsNo code linkedOpen access
preprint2026arXiv

TeamUp: Semantic Project Matching and Team Formation for Learning at Scale

Project-based learning improves student engagement and learning outcomes, yet allocating students to appropriately challenging projects while forming cognitively diverse teams remains difficult at scale. Traditional allocation methods (manual spreadsheets, preference surveys) can't construct the cognitively diverse teams that that collaborate cognitively. This mismatch perpetuates equity issues: high-performing students self-select visible projects while under-represented students face reduced access to opportunity. We propose TeamUp, a lightweight, embedding-based team-forming system designed to improve learning outcomes and equity in large-scale project-based courses. TeamUp uses semantic embeddings from pretrained language models to match students to projects aligned with their skill level. The system employs a hybrid ranking algorithm combining cosine similarity with pedagogical constraints (difficulty alignment, domain preferences, and demand balancing) to generate personalised and transparent recommendations. Beyond individual matching, TeamUp constructs cognitively diverse teams by modelling skill complementarity through embedding variance, ensuring teams possess well-distributed capabilities rather than homogeneous strengths. We evaluated TeamUp through a virtual experiment using 250 student profiles and 60 project descriptions. Results show: (1) substantially higher match quality (mean cosine similarity of 0.74 vs. 0.43); (2) better difficulty alignment (83% placed within one level vs. 34%); (3) more diverse teams (82% covering three or more technical areas vs. 41%); and (4) sub-second recommendation latency at operational costs under $0.10 per student.

0 citations0 reviewsNo code linkedOpen access
preprint2022arXiv

Privacy-Preserving Personalized Fitness Recommender System (P3FitRec): A Multi-level Deep Learning Approach

Recommender systems have been successfully used in many domains with the help of machine learning algorithms. However, such applications tend to use multi-dimensional user data, which has raised widespread concerns about the breach of users privacy. Meanwhile, wearable technologies have enabled users to collect fitness-related data through embedded sensors to monitor their conditions or achieve personalized fitness goals. In this paper, we propose a novel privacy-aware personalized fitness recommender system. We introduce a multi-level deep learning framework that learns important features from a large-scale real fitness dataset that is collected from wearable IoT devices to derive intelligent fitness recommendations. Unlike most existing approaches, our approach achieves personalization by inferring the fitness characteristics of users from sensory data and thus minimizing the need for explicitly collecting user identity or biometric information, such as name, age, height, weight. In particular, our proposed models and algorithms predict (a) personalized exercise distance recommendations to help users to achieve target calories, (b) personalized speed sequence recommendations to adjust exercise speed given the nature of the exercise and the chosen route, and (c) personalized heart rate sequence to guide the user of the potential health status for future exercises. Our experimental evaluation on a real-world Fitbit dataset demonstrated high accuracy in predicting exercise distance, speed sequence, and heart rate sequence compared to similar studies. Furthermore, our approach is novel compared to existing studies as it does not require collecting and using users sensitive information, and thus it preserves the users privacy.

0 citations0 reviewsNo code linkedOpen access
preprint2020arXiv

NeCPD: An Online Tensor Decomposition with Optimal Stochastic Gradient Descent

Multi-way data analysis has become an essential tool for capturing underlying structures in higher-order datasets stored in tensor $\mathcal{X} \in \mathbb{R} ^{I_1 \times \dots \times I_N} $. $CANDECOMP/PARAFAC$ (CP) decomposition has been extensively studied and applied to approximate $\mathcal{X}$ by $N$ loading matrices $A^{(1)}, \dots, A^{(N)}$ where $N$ represents the order of the tensor. We propose a new efficient CP decomposition solver named NeCPD for non-convex problem in multi-way online data based on stochastic gradient descent (SGD) algorithm. SGD is very useful in online setting since it allows us to update $\mathcal{X}^{(t+1)}$ in one single step. In terms of global convergence, it is well known that SGD stuck in many saddle points when it deals with non-convex problems. We study the Hessian matrix to identify theses saddle points, and then try to escape them using the perturbation approach which adds little noise to the gradient update step. We further apply Nesterov's Accelerated Gradient (NAG) method in SGD algorithm to optimally accelerate the convergence rate and compensate Hessian computational delay time per epoch. Experimental evaluation in the field of structural health monitoring using laboratory-based and real-life structural datasets show that our method provides more accurate results compared with existing online tensor analysis methods.

0 citations0 reviewsNo code linkedOpen access
preprint2020arXiv

Online Tensor-Based Learning for Multi-Way Data

The online analysis of multi-way data stored in a tensor $\mathcal{X} \in \mathbb{R} ^{I_1 \times \dots \times I_N} $ has become an essential tool for capturing the underlying structures and extracting the sensitive features which can be used to learn a predictive model. However, data distributions often evolve with time and a current predictive model may not be sufficiently representative in the future. Therefore, incrementally updating the tensor-based features and model coefficients are required in such situations. A new efficient tensor-based feature extraction, named NeSGD, is proposed for online $CANDECOMP/PARAFAC$ (CP) decomposition. According to the new features obtained from the resultant matrices of NeSGD, a new criteria is triggered for the updated process of the online predictive model. Experimental evaluation in the field of structural health monitoring using laboratory-based and real-life structural datasets show that our methods provide more accurate results compared with existing online tensor analysis and model learning. The results showed that the proposed methods significantly improved the classification error rates, were able to assimilate the changes in the positive data distribution over time, and maintained a high predictive accuracy in all case studies.

0 citations0 reviewsNo code linkedOpen access