5 citations · 9 across the 19 of their papers we have counts for
20 papers
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…
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…
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…
Virus2Vec: Viral Sequence Classification Using Machine Learning
Sarwan Ali, Babatunde Bello, Prakash Chourasia +4
Understanding the host-specificity of different families of viruses sheds light on the origin of, e.g., SARS-CoV-2, rabies, and other such zoonotic pathogens in humans. It enables…
ViralVectors: Compact and Scalable Alignment-free Virome Feature Generation
Sarwan Ali, Prakash Chourasia, Zahra Tayebi +2
The amount of sequencing data for SARS-CoV-2 is several orders of magnitude larger than any virus. This will continue to grow geometrically for SARS-CoV-2, and other viruses, as ma…
T Cell Receptor Protein Sequences and Sparse Coding: A Novel Approach to Cancer Classification
Zahra Tayebi, Sarwan Ali, Prakash Chourasia +2
Cancer is a complex disease characterized by uncontrolled cell growth and proliferation. T cell receptors (TCRs) are essential proteins for the adaptive immune system, and their sp…
Efficient Classification of SARS-CoV-2 Spike Sequences Using Federated Learning
Prakash Chourasia, Taslim Murad, Zahra Tayebi +3
This paper presents a federated learning (FL) approach to train an AI model for SARS-Cov-2 variant classification. We analyze the SARS-CoV-2 spike sequences in a distributed way, w…
Anderson Acceleration For Bioinformatics-Based Machine Learning
Sarwan Ali, Prakash Chourasia, Murray Patterson
Anderson acceleration (AA) is a well-known method for accelerating the convergence of iterative algorithms, with applications in various fields including deep learning and optimiza…
Informative Initialization and Kernel Selection Improves t-SNE for Biological Sequences
Prakash Chourasia, Sarwan Ali, Murray Patterson
The t-distributed stochastic neighbor embedding (t- SNE) is a method for interpreting high dimensional (HD) data by mapping each point to a low dimensional (LD) space (usually two-…
Reads2Vec: Efficient Embedding of Raw High-Throughput Sequencing Reads Data
Prakash Chourasia, Sarwan Ali, Simone Ciccolella +2
The massive amount of genomic data appearing for SARS-CoV-2 since the beginning of the COVID-19 pandemic has challenged traditional methods for studying its dynamics. As a result,…
PWM2Vec: An Efficient Embedding Approach for Viral Host Specification from Coronavirus Spike Sequences
Sarwan Ali, Babatunde Bello, Prakash Chourasia +3
COVID-19 pandemic, is still unknown and is an important open question. There are speculations that bats are a possible origin. Likewise, there are many closely related (corona-) vi…