37 citations · 60 across the 52 of their papers we have counts for
8 papers · 1 filter
Uncovering Hierarchical Structure in LLM Embeddings Using Geometric and Topological Measures
Prakash Chourasia, Sarwan Ali, Murray Patterson +1
The rapid advancement of large language models (LLMs) has driven major advances across scientific domains, yet the hierarchical, geometric, and topological structure of their embed…
DPSR: Differentially Private Sparse Reconstruction via Multi-Stage Denoising for Recommender Systems
Sarwan Ali
Differential privacy (DP) has emerged as the gold standard for protecting user data in recommender systems, but existing privacy-preserving mechanisms face a fundamental challenge:…
Boosting t-SNE Efficiency for Sequencing Data: Insights from Kernel Selection
Avais Jan, Prakash Chourasia, Sarwan Ali +1
Dimensionality reduction techniques are essential for visualizing and analyzing high-dimensional biological sequencing data. t-distributed Stochastic Neighbor Embedding (t-SNE) is…
Sequence-to-Image Transformation for Sequence Classification Using Rips Complex Construction and Chaos Game Representation
Sarwan Ali, Taslim Murad, Imdadullah Khan
Traditional feature engineering approaches for molecular sequence classification suffer from sparsity issues and computational complexity, while deep learning models often underper…
Robust Gradient Descent via Heavy-Ball Momentum with Predictive Extrapolation
Sarwan Ali
Accelerated gradient methods like Nesterov's Accelerated Gradient (NAG) achieve faster convergence on well-conditioned problems but often diverge on ill-conditioned or non-convex l…
When do cheap embeddings beat protein language models? A theoretically-grounded hashing sketch for biological sequence classification
Sarwan Ali, Taslim Murad, Imdadullah Khan +1
\textbf{Motivation:} Pre-trained protein language models (PLMs) such as ESM-2 have become the default representation for biological sequence tasks, but they are computationally hea…
Breaking the Euclidean Barrier: Hyperboloid-Based Biological Sequence Analysis
Sarwan Ali, Haris Mansoor, Murray Patterson
Genomic sequence analysis plays a crucial role in various scientific and medical domains. Traditional machine-learning approaches often struggle to capture the complex relationship…
Sequence Analysis Using the Bezier Curve
Taslim Murad, Sarwan Ali, Murray Patterson
The analysis of sequences (e.g., protein, DNA, and SMILES string) is essential for disease diagnosis, biomaterial engineering, genetic engineering, and drug discovery domains. Conv…