5 citations · 12 across the 35 of their papers we have counts for
36 papers
Latent-Kernel Discrete Flow Maps for Few-Step Generation
Mansoor Ahmed, Yue-Tsz Fan, Hemanth Venkateswara +1
Discrete diffusion and flow-matching models denoise a sequence over many steps, but to keep each step cheap, they factorize the transition across positions and decide every token i…
EpiFormer: Learning Antigen-Antibody Interactions for Epitope Prediction via Geometric Deep Learning
Mansoor Ahmed, Huirong Chai, Haoxin Wang +2
Antibodies neutralize foreign antigens by binding to specific surface regions called epitopes. Computational epitope prediction is critical for understanding immune recognition and…
EvoStruct: Bridging Evolutionary and Structural Priors for Antibody CDR Design via Protein Language Model Adaptation
Mansoor Ahmed, Sujin Lee, Umar Khayaz +1
Equivariant graph neural network (GNN) methods for antibody complementarity-determining region (CDR) design achieve the highest sequence recovery but suffer from severe vocabulary…
AgForce Enables Antigen-conditioned Generative Antibody Design
Mansoor Ahmed, Murray Patterson
Antibody design methods condition on antigen structure to generate complementarity-determining regions (CDR), yet a systematic evaluation of baseline methods reveals that they larg…
ConTact: Contact-First Antibody CDR Design via Explicit Interface Reasoning
Mansoor Ahmed, Spencer VonBank, Nadeem Taj +3
Computational antibody CDR design methods condition on antigen structure to generate binding loops. Yet, the existing architectures conflate two fundamentally distinct sub-problems…
CHIMERA-Bench: A Benchmark Dataset for Epitope-Specific Antibody Design
Mansoor Ahmed, Nadeem Taj, Imdad Ullah Khan +2
Computational antibody design has seen rapid methodological progress, with dozens of deep generative methods proposed in the past three years, yet the field lacks a standardized be…
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…
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…
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…
Sequence-Based Nanobody-Antigen Binding Prediction
Usama Sardar, Sarwan Ali, Muhammad Sohaib Ayub +4
Nanobodies (Nb) are monomeric heavy-chain fragments derived from heavy-chain only antibodies naturally found in Camelids and Sharks. Their considerably small size (~3-4 nm; 13 kDa)…
Robust Brain Age Estimation via Regression Models and MRI-derived Features
Mansoor Ahmed, Usama Sardar, Sarwan Ali +3
The determination of biological brain age is a crucial biomarker in the assessment of neurological disorders and understanding of the morphological changes that occur during aging.…
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…