37 citations · 60 across the 52 of their papers we have counts for
59 papers
Auditing pretraining contamination in single-cell foundation model benchmarks
Sarwan Ali
Single-cell foundation models (scFMs) such as Geneformer, scGPT, and Universal Cell Embeddings (UCE) are pretrained on tens of millions of cells drawn from public repositories. The…
Causal dictionary learning reveals and validates transcription-factor binding features in genomic language models
Sarwan Ali
Genomic language models achieve strong performance across regulatory-genomics tasks, yet what these models internally represent remains opaque, and the field lacks a principled pro…
Multi-Scale Reversible Chaos Game Representation: A Unified Framework for Sequence Classification
Sarwan Ali, Taslim Murad
Biological classification with interpretability remains a challenging task. For this, we introduce a novel encoding framework, Multi-Scale Reversible Chaos Game Representation (MS-…
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…
Converting Time Series Data to Numeric Representations Using Alphabetic Mapping and k-mer strategy
Sarwan Ali, Tamkanat E Ali, Imdad Ullah Khan +1
In the realm of data analysis and bioinformatics, representing time series data in a manner akin to biological sequences offers a novel approach to leverage sequence analysis techn…
Hilbert Curve Based Molecular Sequence Analysis
Sarwan Ali, Tamkanat E Ali, Imdad Ullah Khan +1
Accurate molecular sequence analysis is a key task in the field of bioinformatics. To apply molecular sequence classification algorithms, we first need to generate the appropriate…
Neuromorphic Spiking Neural Network Based Classification of COVID-19 Spike Sequences
Taslim Murad, Prakash Chourasia, Sarwan Ali +2
The availability of SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) virus data post-COVID has reached exponentially to an enormous magnitude, opening research doors to…
Computing Gram Matrix for SMILES Strings using RDKFingerprint and Sinkhorn-Knopp Algorithm
Sarwan Ali, Haris Mansoor, Prakash Chourasia +2
In molecular structure data, SMILES (Simplified Molecular Input Line Entry System) strings are used to analyze molecular structure design. Numerical feature representation of SMILE…
DWFL: Enhancing Federated Learning through Dynamic Weighted Averaging
Prakash Chourasia, Tamkanat E Ali, Sarwan Ali +1
Federated Learning (FL) is a distributed learning technique that maintains data privacy by providing a decentralized training method for machine learning models using distributed b…
EPIC: Enhancing Privacy through Iterative Collaboration
Prakash Chourasia, Heramb Lonkar, Sarwan Ali +1
Advancements in genomics technology lead to a rising volume of viral (e.g., SARS-CoV-2) sequence data, resulting in increased usage of machine learning (ML) in bioinformatics. Trad…
MIK: Modified Isolation Kernel for Biological Sequence Visualization, Classification, and Clustering
Sarwan Ali, Prakash Chourasia, Haris Mansoor +2
The t-Distributed Stochastic Neighbor Embedding (t-SNE) has emerged as a popular dimensionality reduction technique for visualizing high-dimensional data. It computes pairwise simi…
Position Specific Scoring Is All You Need? Revisiting Protein Sequence Classification Tasks
Sarwan Ali, Taslim Murad, Prakash Chourasia +4
Understanding the structural and functional characteristics of proteins are crucial for developing preventative and curative strategies that impact fields from drug discovery to po…
DANCE: Deep Learning-Assisted Analysis of Protein Sequences Using Chaos Enhanced Kaleidoscopic Images
Taslim Murad, Prakash Chourasia, Sarwan Ali +2
Cancer is a complex disease characterized by uncontrolled cell growth. T cell receptors (TCRs), crucial proteins in the immune system, play a key role in recognizing antigens, incl…
Nearest Neighbor CCP-Based Molecular Sequence Analysis
Sarwan Ali, Prakash Chourasia, Bipin Koirala +1
Molecular sequence analysis is crucial for comprehending several biological processes, including protein-protein interactions, functional annotation, and disease classification. Th…
Expanding Chemical Representation with k-mers and Fragment-based Fingerprints for Molecular Fingerprinting
Sarwan Ali, Prakash Chourasia, Murray Patterson
This study introduces a novel approach, combining substruct counting, -mers, and Daylight-like fingerprints, to expand the representation of chemical structures in SMILES string…
A Universal Non-Parametric Approach For Improved Molecular Sequence Analysis
Sarwan Ali, Tamkanat E Ali, Prakash Chourasia +1
In the field of biological research, it is essential to comprehend the characteristics and functions of molecular sequences. The classification of molecular sequences has seen wide…
A Memetic Algorithm To Find a Hamiltonian Cycle in a Hamiltonian Graph
Sarwan Ali, Pablo Moscato
We present a memetic algorithm (\maa) approach for finding a Hamiltonian cycle in a Hamiltonian graph. The \ma is based on a proven approach to the Asymmetric Travelling Salesman P…