Zubair Saeed

Postdoctoral Associate
CV
Zubair.pdf
ORCiD
0000-0001-5302-7133
GitHub
zubi00
Google Scholar
Zubair Saeed
Email
zubairsaeed602obfuscate@gmail.com

Short Bio

Zubair Saeed is a Postdoctoral Associate at Florida International University (FIU) in the Knight Foundation School of Computing and Information Sciences (KFSCIS). Dr. Zubair earned his PhD in Electrical & Computer Engineering from the Texas A&M in 2026. He has strong academic background and extensive research contributions. With notable expertise in computer vision, machine learning, and deep learning, he has published peer-reviewed research papers on various topics, including disease detection, small object detection, and cancer detection. He has been invited to review many peer-reviewed journals and IEEE proceeding articles. Proficient in Python, C/C++, and LaTeX, his diverse skill set, and research acumen make him an asset in the realm of Artificial Intelligence.

RESEARCH AND EDUCATIONAL INTERESTS

AI for Health and Biomedical Imaging, Machine Learning and Deep Learning

EDUCATION

Postdoctoral Training, Florida International University (FIU), Knight Foundation School of Computing and Information Sciences (KFSCIS), Miami, Florida, USA. (2026 - Present)

PhD, Electrical and Computer Engineering, Texas A&M University, College Station, TX, USA.(2023-2025)

MS Engg, Computer Engineering, University of Engineering and Technology (UET), Taxila. (2020-2023)

BS Engg, Computer Engineering, Heavy Industry Taxila Education City (HITEC), Taxila. (2016-2020)

Research
Papers

  1. ProteoRift Protocols: A Deep Learning Filtering Workflow for Peptide Identification in Mass Spectrometry Data

  2. ProtEnrich: Residual Multimodal Enrichment of Protein Sequence Embeddings

  3. CViT-ESP: Lightweight Pre-trained Vision Transformers for EEG-based Epileptic Seizure Prediction

  4. BindScreen: Protein-Centric Contrastive Learning for Sequence-Based Virtual Screening

  5. TITAN-BBB: Predicting BBB Permeability using Multi-Modal Deep-Learning Models

  6. MolDeBERTa: Foundational Model for Physicochemical and Structural-Informed Molecular Representation Learning

  7. Habenula alterations in resting state functional connectivity among autistic individuals

  8. Predicting progression of Alzheimer’s disease using blood-based multi-omics data

  9. End-to-end deep attention-based multitask pipeline for predicting uncertainty-quantified peptide properties from mass spectrometry data

  10. A Machine Learning and Benchmarking Approach for Molecular Formula Assignment of Ultra High-Resolution Mass Spectrometry Data from Complex Mixtures

  11. FiCOPS: Hardware and Software Co-Design of FPGA Computational Framework for Mass Spectrometry-Based Peptide Database Search

  12. Systems and methods for patient-specific epileptic seizure prediction

  13. fairGNN-WOD: fair graph learning without demographics

  14. RAPTOR: Reconfigurable Advanced Platform for Trans- disciplinary Open Research

  15. Overcoming Site Variability in Multisite fMRI Studies: An Autoencoder Framework for Enhanced Generalizability of Machine Learning Models

  16. MLSPred-Bench: Transforming Electroencephalography (EEG) Datasets into Machine Learning-Ready Seizure Prediction Benchmarks

  17. Machine-learning models for Alzheimer’s disease diagnosis using neuroimaging data: survey, reproducibility, and generalizability evaluation

  18. TA‐RNN: an Attention‐based Time‐aware Recurrent Neural Network Architecture to Predict Progression of Alzheimer’s Disease

  19. Alzheimer’s disease-associated gene ranking using PhenoGeneRanker

  20. Alzheimer’s disease diagnosis using gray matter of T1-weighted sMRI data and vision transformer

  21. Predicting Individual’s Cognitive Performance Through Multi-Omics Blood Data Using Hierarchical Input Neural Network - HINN

  22. HINN prioritizes multi-omics biomarkers associated with cognitive decline

  23. Robustness of ML-Based Seizure Prediction Using Noisy EEG Data From Limited Channels

  24. Lightweight Transformer exhibits comparable performance to LLMs for Seizure Prediction: A case for light-weight models for EEG data

  25. Utilizing Pretrained Vision Transfomers and Large Language Models for Epileptic Seizure Prediction

  26. PVTAD: Alzheimer’s Disease Diagnosis Using Pyramid Vision Transformer Applied to White Matter of T1-Weighted Structural MRI Data

  27. Making MS Omics Data ML-Ready: SpeCollate Protocols

  28. Heterogeneity Aware Distributed Machine Learning at the Wireless Edge for Health IoT Applications: An EEG Data Case Study

  29. Communication Evaluation of a Wireless 4-Channel Wearable EEG for Brain-Computer Interface (BCI) and Healthcare Applications

  30. Systems and methods for matching mass spectrometry data with a peptide database

  31. Statistical and Machine Learning Analysis of the Human Brain Functional Network in a Multi-Site Resting-State Functional MRI Database Framework

  32. Q-CASA Invited Speakers Quantum-Centric Supercomputing Strategies for Neuroscience problems: Challenges and Progress

  33. PPAD: a deep learning architecture to predict progression of Alzheimer’s disease

  34. High Performance Computing Algorithms for Accelerating Peptide Identification from Mass-Spectrometry Data Using Heterogeneous Supercomputers

  35. GPU-acceleration of the distributed-memory database peptide search of mass spectrometry data

  36. Energy Efficient AI/ML based Continuous Monitoring at the Edge: ECG and EEG Case Study

  37. Description of Dissolved Organic Matter Transformational Networks at the Molecular Level

  38. Confounding Effects on the Performance of Machine Learning Analysis of Static Functional Connectivity Computed from rs-fMRI Multi-site Data

  39. ASD-GResTM: Deep Learning Framework for ASD classification using Gramian Angular Field

  40. 22nd IEEE International Workshop on High Performance Computational Biology (HiCOMB 2023)

  41. Unsupervised structural classification of dissolved organic matter based on fragmentation pathways

  42. Systems and methods for peptide identification

  43. Systems and methods for measuring similarity between mass spectra and peptides

  44. Systems And Methods For Diagnosing Autism Spectrum Disorder Using fMRI Data

  45. SPERTL: Epileptic Seizure Prediction using EEG with ResNets and Transfer Learning

  46. Re-configurable Hardware for Computational Proteomics

  47. Need for High-Performance Computing for MS-Based Omics Data Analysis

  48. Molecular level characterization of DOM along a freshwater-to-estuarine coastal gradient in the Florida Everglades

  49. Machine-Learning and the Future of HPC for MS-Based Omics

  50. Introduction to Mass Spectrometry Data

  51. High-Performance Computing Strategy Using Distributed-Memory Supercomputers

  52. High-Performance Algorithms for Mass Spectrometry-Based Omics

  53. G-MSR: A GPU-Based Dimensionality Reduction Algorithm

  54. Fast Spectral Pre-processing for Big MS Data

  55. Existing HPC Methods and the Communication Lower Bounds for Distributed-Memory Computations for Mass Spectrometry-Based Omics Data

  56. Computational CPU-GPU Template for Pre-processing of Floating-Point MS Data

  57. Communication lower-bounds for distributed-memory computations for mass spectrometry based omics data

  58. Classification of Autism Spectrum Disorder Using rs-fMRI data and Graph Convolutional Networks

  59. Biomedical IoT: Enabling Technologies, Architectural Elements, Challenges, and Future Directions

  60. A Easy to Use Generalized Template to Support Development of GPU Algorithms

  61. TurboBFS: GPU Based Breadth-First Search (BFS) Algorithms in the Language of Linear Algebra

  62. TurboBC: A Memory Efficient and Scalable GPU Based Betweenness Centrality Algorithm in the Language of Linear Algebra

  63. SpeCollate: Deep cross-modal similarity network for mass spectrometry data based peptide deductions

  64. Source data: high performance computing framework for tera-scale database search of mass spectrometry data

  65. Simulation Testbed for Evaluating Distributed Querying and Searching of Mass Spectrometry Big Data in a Network-based Infrastructure

  66. Search feasibility in distributed MS-proteomics big data

  67. Real-time peptide identification from high-throughput mass-spectrometry data

  68. Methods for Proteogenomics Data Analysis, Challenges, and Scalability Bottlenecks: A Survey

  69. Machine Learning methods for diagnosing Autism Spectrum Disorder and Attention-deficit/Hyperactivity Disorder using functional and structural MRI: A Survey

  70. High performance computing framework for tera-scale database search of mass spectrometry data

  71. HiCOPS: High Performance Computing Framework for Tera-Scale Database Search of Mass Spectrometry based Omics Data

  72. Graph Theoretic Approach for the Analysis of Comprehensive Mass-Spectrometry (MS/MS) Data of Dissolved Organic Matter

  73. Explainable and scalable machine learning algorithms for detection of autism spectrum disorder using fMRI data

  74. DeepCOVIDNet: Deep Convolutional Neural Network for COVID-19 Detection from Chest Radiographic Images

  75. Communication-avoiding micro-architecture to compute Xcorr scores for peptide identification

  76. Benchmarking mass spectrometry based proteomics algorithms using a simulated database

  77. ASD-SAENet: a sparse autoencoder, and deep-neural network model for detecting autism spectrum disorder (ASD) using fMRI data

  78. A Multi-Factorial Assessment of Functional Human Autistic Spectrum Brain Network Analysis

  79. ASD-DiagNet: A Hybrid Learning Approach for Detection of Autism Spectrum Disorder Using fMRI Data

  80. NGS-Integrator: An efficient tool for combining multiple NGS data tracks using minimum Bayes’ factors

  81. Methods and systems for compressing data

  82. Federated learning: A survey on enabling technologies, protocols, and applications

  83. Slm-transform: A method for memory-efficient indexing of spectra for database search in lc-ms/ms proteomics

  84. Optimized CNN-based diagnosis system to detect the pneumonia from chest radiographs

  85. NGS‐Integrator: A Tool for Combining Information from Multiple Genome‐Wide NGS Data Tracks Using Minimum Bayes Factors

  86. LBE: A Computational Load Balancing Algorithm for Speeding up Parallel Peptide Search in Mass-Spectrometry based Proteomics

  87. GPU-SFFT: A GPU based parallel algorithm for computing the Sparse Fast Fourier Transform (SFFT) of k-sparse signals

  88. GPU-DFC: A GPU-based parallel algorithm for computing dynamic-functional connectivity of big fMRI data

  89. Efficient shared peak counting in database peptide search using compact data structure for fragment-ion index

  90. Auto-ASD-Network: A technique based on Deep Learning and Support Vector Machines for diagnosing Autism Spectrum Disorder using fMRI data

  91. ASD-DiagNet: A hybrid learning approach for detection of Autism Spectrum Disorder using fMRI data

  92. 2019 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)

  93. Towards quantifying psychiatric diagnosis using machine learning algorithms and big fMRI data

  94. Similarity based classification of ADHD using Singular Value Decomposition

  95. Parallel sampling-pipeline for indefinite stream of heterogeneous graphs using OpenCL for FPGAs

  96. MaSS‐Simulator: A Highly Configurable Simulator for Generating MS/MS Datasets for Benchmarking of Proteomics Algorithms

  97. GPU-DAEMON: GPU algorithm design, data management & optimization template for array based big omics data

  98. Fast-GPU-PCC: A GPU-Based Technique to Compute Pairwise Pearson’s Correlation Coefficients for Time Series Data - An fMRI Study

  99. A Fourier-Based Data Minimization Algorithm for Fast and Secure Transfer of Big Genomic Datasets

  100. A deep learning-based data minimization algorithm for fast and secure transfer of big genomic datasets

  101. Scalable data structure to compress next-generation sequencing files and its application to compressive genomics

  102. Power-Efficient and Highly Scalable Parallel Graph Sampling using FPGAs

  103. GPU-PCC: A GPU Based Technique to Compute Pairwise Pearson's Correlation Coefficients for Big fMRI Data

  104. An out-of-core gpu based dimensionality reduction algorithm for big mass spectrometry data and its application in bottom-up proteomics

  105. A new cryptography algorithm to protect cloud-based healthcare services

  106. A Hybrid MPI-OpenMP Strategy to Speedup the Compression of Big Next-Generation Sequencing Datasets

  107. Systems-level analysis reveals selective regulation of Aqp2 gene expression by vasopressin

  108. Reductive Analytics on Big MS Data leads to tremendous reduction in time for peptide deduction

  109. MS-REDUCE: an ultrafast technique for reduction of big mass spectrometry data for high-throughput processing

  110. Introduction to the selected papers from the 7th International Conference on Bioinformatics and Computational Biology (BICoB 2015)

  111. GPU-ArraySort: A parallel, in-place algorithm for sorting large number of arrays

  112. Data Aware Communication for Energy Harvesting Sensor Networks

  113. A variable-length network encoding protocol for big genomic data

  114. A Parallel Peptide Indexer and Decoy Generator for Crux Tide using OpenMP

  115. On the sampling of big mass spectrometry data

  116. Design and implementation of network transfer protocol for big genomic data

  117. Big data proteogenomics and high performance computing: Challenges and opportunities

  118. Autophagic degradation of aquaporin-2 is an early event in hypokalemia-induced nephrogenic diabetes insipidus

  119. A parallel algorithm for compression of big next-generation sequencing datasets

  120. Global analysis of the effects of the V2 receptor antagonist satavaptan on protein phosphorylation in collecting duct

  121. Foreword to the special issue on selected papers from the 6th International Conference on Bioinformatics and Computational Biology (BICoB 2014).

  122. Exploiting thread-level and instruction-level parallelism to cluster mass spectrometry data using multicore architectures

  123. Cams-rs: clustering algorithm for large-scale mass spectrometry data using restricted search space and intelligent random sampling

  124. A knowledge base of vasopressin actions in the kidney

  125. 6th International Conference on Bioinformatics and Computational Biology (BICoB 2014)

  126. Quantitative phosphoproteomics implicates clusters of proteins involved in cell‐cell adhesion and transcriptional regulation in the vasopressin signaling network

  127. Proteome-wide measurement of protein half-lives and translation rates in vasopressin-sensitive collecting duct cells

  128. PhosSA: Fast and accurate phosphorylation site assignment algorithm for mass spectrometry data

  129. Foreword to the special issue on selected papers from the 5th International Conference on Bioinformatics and Computational Biology (BICoB 2013)

  130. A high performance algorithm for clustering of large-scale protein mass spectrometry data using multi-core architectures

  131. A Graphical User Interface (GUI) for Phosphorylation Site Assignment of Protein Mass Spectrometry Data

  132. Quantitative phosphoproteomics in nuclei of vasopressin-sensitive renal collecting duct cells

  133. Proteomic and Metabolomic Approaches to Cell Physiology and Pathophysiology: Quantitative phosphoproteomics in nuclei of vasopressin-sensitive renal collecting duct cells

  134. NHLBI-AbDesigner: an online tool for design of peptide-directed antibodies

  135. Identifying protein kinase target preferences using mass spectrometry

  136. High performance phosphorylation site assignment algorithm for mass spectrometry data using multicore systems

  137. Dynamics of the G protein-coupled vasopressin V2 receptor signaling network revealed by quantitative phosphoproteomics

  138. CP hos: a program to calculate and visualize evolutionarily conserved functional phosphorylation sites

  139. An efficient dynamic programming algorithm for phosphorylation site assignment of large-scale mass spectrometry data

  140. An efficient algorithm for clustering of large-scale mass spectrometry data

  141. A high performance multiple sequence alignment system for pyrosequencing reads from multiple reference genomes

  142. Mining temporal patterns from iTRAQ mass spectrometry (LC-MS/MS) data

  143. Mapping‐based temporal pattern mining algorithm (MTPMA) identifies unique clusters of phosphopeptides regulated by vasopressin in collecting duct

  144. Large‐scale iTRAQ‐based quantification of phosphorylation changes during vasopressin signaling

  145. Parallel Algorithm for Center Star Sequence and Alignments with Applications to Short Reads

  146. High performance computational biology algorithms

  147. A graph-theoretic framework for efficient computation of HMM based motif finder

  148. Pyro-align: Sample-align based multiple alignment system for pyrosequencing reads of large number

  149. Multiple sequence alignment system for pyrosequencing reads

  150. An Overview of Multiple Sequence Alignment Systems

  151. A domain decomposition strategy for alignment of multiple biological sequences on multiprocessor platforms

  152. Sample-align-d: A high performance multiple sequence alignment system using phylogenetic sampling and domain decomposition