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Saeed Ahmed

PhD in Computer Science and Technology (Bioinformatics)

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About Me

(اَلسَّلَامُ عَلَيْكُم‎) I am an Assistant Professor of Computer Science and a researcher in Bioinformatics and Artificial Intelligence, focusing on protein, peptide, and genomic sequence analysis.

I earned my PhD in Computer Science and Technology from NJUST, China (2021), where my research explored post-translational modifications and cancer-type prediction using machine learning and deep learning techniques.

I completed postdoctoral research at Mahidol University (Thailand), working on therapeutic peptide prediction and DNA/RNA sequence modeling, followed by research at Lund University (Sweden), where I developed advanced computational models for gain- and loss-of-function mutation analysis in the human genome.

I previously served as an Assistant Professor at the University of Management and Technology (UMT), supervising BS and MS research in AI, bioinformatics, computer vision, and data science.

My current research focuses on advanced AI-driven solutions for biological data, including multimodal learning frameworks that integrate sequence, structural, and biochemical features.

I actively work with pretrained models, large language models (LLMs), and transformer-based architectures to extract meaningful representations from biological sequences and improve predictive performance in complex bioinformatics tasks.

I have authored 47+ research publications and have strong expertise in PyTorch, TensorFlow, and scikit-learn, along with emerging areas such as explainable AI, protein language models, and biomedical data mining.

Biography

Contact

saeedcs@uoswabi.edu.pk

saeed.ahmad075@gmail.com

Phone

+923443820531

Address
Permanent Address

Village and P.O Nawagai, Tehsil Mandanr,
District Buner, Khyber Pakhtunkhwa,
Pakistan

Work Address

Department of Computer Science,
University of Swabi,
Swabi, Khyber Pakhtunkhwa,
Pakistan

Skills

Bioinformatics • Machine Learning • Deep Learning • Multimodal Learning • Transformer Models • Large Language Models • Biomedical Imaging • Protein Sequence Analysis • Data Science

Languages

English (Fluent), Urdu (Native), Pashto (Mother Tongue)

Collaboration

Open to research collaborations in Bioinformatics, Artificial Intelligence, Multimodal Learning, and Transformer-based Biomedical Applications.

Work Experience:

  1. Assistant ProfessorCurrent

    Department of Computer Science
    University of Swabi, Pakistan

  2. Postdoctoral ResearcherCurrent

    Center for Research Innovation and Biomedical Informatics, Faculty of Medical Technology
    Mahidol University, Bangkok, 10700, Thailand

  3. Postdoctoral Research Fellow

    Biomedical Center (BMC)
    Lund University, Sweden

  4. Assistant Professor

    Department of Computer Sciences, SST
    University of Management and Technology (UMT), Lahore, Pakistan

  5. Postdoctoral Research Fellow

    Center of Data Mining and Biomedical Informatics
    Mahidol University, Bangkok, Thailand

Education:

  1. PhD in Computer Science and Technology  

    from the School of Computer Science & Engineering
    Nanjing University of Science and Technology, Nanjing, China

    Dissertation: Research on Prediction of Protein Phosphorylation and Cancer Subtypes via Intelligent Computation.

  2. MS Computer Science  

    from Department of Computer Science
    Abdul Wali Khan University Mardan, KP, Pakistan.

    Thesis: Identification of Heat Shock Protein Families and J-Protein Types using Dipeptide Composition and Support Vector Machine.

  3. Bachelor of Science in Telecommunication  

    from Institute of Engineering and Computing Sciences (IECS)
    University of Science and Technology, Bannu, KhyberPakhtunKhawa, Pakistan.

Research Interests:

  1. Bioinformatics and Computational Biology

  2. Machine Learning and Deep Learning for Biological Data

  3. Multimodal Learning for Biological Data Integration

  4. Transformer Models and Protein Language Models

  5. Large Language Models (LLMs) in Bioinformatics

  6. Protein and Peptide Sequence Analysis

  7. Genomic Data Modeling and Mutation Analysis

  8. Explainable AI (XAI) for Biomedical Applications

  9. AI for Drug Discovery and Therapeutic Design

Research Publications:

  1. Publications  2026

    1. Saeed Ahmed, [Other Authors Names]; [Your Paper Title Here], [J] [Journal Name], Volume [Volume Number], Issue [Issue Number], 2026, Pages [Page Numbers]. [Publisher Name]

  2. Publications  2025

    1. Saeed Ahmed, N Schaduangrat, C Pipattanaboon, W Shoombuatong; Accurate identification of broadly neutralizing antibodies against dengue virus based on deep stacking strategy with multi-perspective features, [J] Scientific Reports, 2025, Pages bbab583. Nature Publishing Group UK

    2. Saeed Ahmed, N Schaduangrat, P Chumnanpuen, SM H Mahmud, K O Michae Goh, W Shoombuatong; BLSAM-TIP: Improved and robust identification of tyrosinase inhibitory peptides by integrating bidirectional LSTM with self-attention mechanism, [J] PloS one, Volume 20, Issue 10, 2025, Pages e0333614. Public Library of Science

    3. Saeed Ahmed, N Schaduangrat, I Meewan, W Shoombuatong; DeepHDAC3i: Leveraging an Interpretable Deep Learning-based Framework for the Accelerated Discovery of HDAC3 Inhibitors, [J] IEEE Transactions on Computational Biology and Bioinformatics, Volume 22, Issue 6, 2025, Pages 2453-2464. IEEE

    4. Saeed Ahmed, N Schaduangrat, P Chumnanpuen, W Shoombuatong; GRU4ACE: Enhancing ACE inhibitory peptide prediction by integrating gated recurrent unit with multi‐source feature embeddings, [J] Protein Science, Volume 3346, Issue 6, 2025, Pages e70026. John Wiley & Sons, Inc.

    5. M Gill, M Kabir, Saeed Ahmed, M A Subhani, M Hayat; A Comparative Review and Analysis of Computational Predictors for Identification of Enhancer and their Strength, [J] Current Bioinformatics, Volume 20, Issue 4, 2025, Pages 323-343. Bentham Science Publishers

    6. W Shoombuatong, Saeed Ahmed, SM H Mahmud, N Schaduangrat; A comprehensive review and evaluation of machine learning-based approaches for identifying tumor T cell antigens, [J] Computational Biology and Chemistry, Volume 18, 2025, Pages 108440. Elsevier

    7. W Shoombuatong, N Schaduangrat, N Homdee, Saeed Ahmed, P Chumnanpuen; Advancing the accuracy of tyrosinase inhibitory peptides prediction via a multiview feature fusion strategy, [J] Scientific Reports, Volume 15, Issue 1, 2025, Pages 4762. Nature Publishing Group UK

    8. H Zhang, M Kabir, Saeed Ahmed, M Vihinen; There will always be variants of uncertain significance. Analysis of VUSs, [J] NAR Genomics and Bioinformatics, Volume 6, Issue 4, 2025, Pages lqae154. Oxford University Press

    9. W Shoombuatong, N Schaduangrat, N Homdee, Saeed Ahmed, P Chumnanpuen; Advancing the Accuracy of Anti-MRSA Peptide Prediction Through Integrating MultiSource Protein Language Models, [J] Scientific Reports, Volume 15, Issue 1, 2025, Pages 4762. Nature Publishing Group UK

    10. M Kabir, Saeed Ahmed, H Zhang, I Rodríguez-Rodríguez, S M Najibi, M Vihinen; PON-P3: Accurate Prediction of Pathogenicity of Amino Acid Substitutions, [J] International Journal of Molecular Sciences, Volume 26, 2025, Pages 2004.

  3. Publications  2024

    1. A Amjad, Saeed Ahmed, M Arif, T Alam, M Kabir*; A novel deep learning identifier for promoters and their strength using heterogeneous features, [J] Methods, Volume 230, 2024, Pages 119-128.

    2. M A Arshed, S Mumtaz, Stefan C Gherghina, N Urooj, Saeed Ahmed, C Dewi*; A Deep Learning Model for Detecting Fake Medical Images to Mitigate Financial Insurance Fraud, [J] Computation, Volume 12, Issue 9, 2024, Pages 173.

    3. R Arif, Saeed Ahmed, S Kanwal, M Kabir*; A Computational Predictor for Accurate Identification of Tumor Homing Peptides by Integrating Sequential and Deep BiLSTM Features, [J] Interdisciplinary Sciences: Computational Life Sciences, 2024, Pages 1-16.

    4. F Arshad, A Amjad, Saeed Ahmed, M Kabir*; An explainable stacking-based approach for accelerating the prediction of antidiabetic peptides, [J] Analytical Biochemistry, 2024, Pages 115546.

    5. S Kanwal, R Arif, Saeed Ahmed, M Kabir*; A novel stacking-based predictor for accurate prediction of antimicrobial peptides, [J] Journal of Biomolecular Structure and Dynamics, Taylor & Francis, 2024, Pages 1-12.

    6. M A Arshed, H A Rehman, Saeed Ahmed, C Dewi, H J Christanto; A 16 × 16 Patch-Based Deep Learning Model for the Early Prognosis of Monkeypox from Skin Color Images, [J] Computation - MDPI, Volume 12, Issue 2, 2024, Pages 33.

    7. M. A. Arshed, S. Mumtaz, M. Ibrahim, C. Dewi, M. Tanveer, Saeed Ahmed; Multiclass AI-Generated Deepfake Face Detection Using Patch-Wise Deep Learning Model, [J] Computers- MDPI, Volume 13, Issue 1, 2024, Pages 31.

  4. Publications  2023

    1. Mehwish Gill, Saeed Ahmad, Muhammad Kabir*, Maqsood Hayat; A Novel Predictor for the Analysis and Prediction of Enhancers and Their Strength via Multi-View Features and Deep Forest, [J] Information - MDPI, Volume 14, Issue 12, 2023, Pages 636.

    2. M A Arshed, M Ibrahim, S Mumtaz, M Tanveer, Saeed Ahmed; Chem2Side: A Deep Learning Model with Ensemble Augmentation (Conventional+ Pix2Pix) for COVID-19 Drug Side-Effects Prediction from Chemical Images, [J] Information - MDPI, Volume 14, Issue 12, 2023, Pages 663.

    3. M. A. Arshed, S. Mumtaz, M. Ibrahim, Saeed Ahmed, M Tahir, M. Shafi; Multi-class skin cancer classification using vision transformer networks and convolutional neural network-based pre-trained models, [J] Information - MDPI, Volume 14, Issue 7, 2023, Pages 415.

    4. Hina Alam, Muhammad Burhan, Anusha Gillani, Ihtisham ul Haq, Muhammad Asad Arshed, Muhammad Shafi, Saeed Ahmed; IoT Based Smart Baby Monitoring System with Emotion Recognition Using Machine Learning, [J] Wireless Communications and Mobile Computing - Hindawi, Volume 2023, 2023, Pages 1175450.

  5. Publications  2022

    1. Saeed Ahmed, Muhammad Arif, Muhammad Kabir*, Khaistah Khan, Yaser Daanial Khan; PredAoDP: Accurate identification of antioxidant proteins by fusing different descriptors based on evolutionary information with support vector machine, [J] Chemometrics and Intelligent Laboratory Systems, Volume 228, 2022, Pages 104623.

    2. Phasit Charoenkwan, Saeed Ahmed, Chanin Nantasenamat, Julian MW Quinn, Mohammad Ali Moni, Pietro Lio’, Watshara Shoombuatong*; AMYPred-FRL is a novel approach for accurate prediction of amyloid proteins by using feature representation learning, [J] Scientific reports, 2022, Pages 7697.

    3. Saeed Ahmad, Phasit Charoenkwan, Julian MW Quinn, Mohammad Ali Moni, Md Mehedi Hasan, Pietro Lio’, Watshara Shoombuatong*; SCORPION is a stacking-based ensemble learning framework for accurate prediction of phage virion proteins, [J] Scientific Reports, 2022, Pages 4106.

    4. Muhammad Arif, Saeed Ahmad, Fang Ge, Muhammad Kabir*, Yaser Daniaal Khan, Dong-Jun Yu*, Maha Thafar; StackACPred: Prediction of anticancer peptides by integrating optimized multiple feature descriptors with stacked ensemble approach, [J] Chemometrics and Intelligent Laboratory Systems, Volume 220, 2022, Pages 10445815.

  6. Publications  2021

    1. Saeed Ahmad, Muhammad Kabir, Muhammad Arif, Zaheer Ullah Khan, Dong-Jun Yu*; DeepPPSite: A deep learning based model for analysis and prediction of phosphorylation sites using efficient sequence information, [J] Analytical Biochemistry, Volume 612, 2021, Pages 113955.

    2. Muhammad Arif, Muhammad Kabir, Saeed Ahmad, Abid Khan, Fang Ge, Adel Khelifi, Dong-Jun Yu; DeepCPPred: a deep learning framework for the discrimination of cell-penetrating peptides and their uptake efficiencies, [J] IEEE/ACM Transactions on Computational Biology and Bioinformatics, Volume 19, Issue 5, 2021, Pages 2749-2759.

  7. Publications  2020

    1. Saeed Ahmad, Muhammad Kabir*, Muhammad Arif, Zakir Ali, Zar Nawab Khan Swati; Prediction of human phosphorylated proteins by extracting multi-perspective discriminative features from the evolutionary profile and physicochemical properties through LFDA, [J] Chemometrics and Intelligent Laboratory Systems, Volume 203, 2020, Pages 104066.

    2. Muhammad Arif, Saeed Ahmad, Farman Ali, Ge Fang, Min Li, Dong-Jun Yu*; TargetCPP: accurate prediction of cell-penetrating peptides from optimized multi-scale features using gradient boost decision tree, [J] Journal of computer-aided molecular design, Volume 34, 2020, Pages 841-856.

    3. Muhammad Arif, Farman Ali, Saeed Ahmad, Muhammad Kabir, Zakir Ali, Maqsood Hayat*; Pred-BVP-Unb: Fast Prediction of Bacteriophage Virion Proteins Using Un-biased Multi-perspective Properties with Recursive Feature Elimination, [J] Genomics, Volume 112, Issue 2, 2020, Pages 1565-1574.

    4. Muhammad Kabir*, Muhammad Iqbal, Saeed Ahmad, Maqsood Hayat*; iNR-2L: A two-level sequence-based predictor developed via Chou’s 5-steps rule and general PseAAC for identifying nuclear receptors and their families, [J] Genomics, Volume 112, Issue 1, 2020, Pages 276-285.

    5. Farman Ali, Muhammad Arif, Zaheer Ullah Khan, Muhammad Kabir, Saeed Ahmad, Dong-Jun Yu*; SDBP-Pred: Prediction of single-stranded and double-stranded DNA-binding proteins by extending consensus sequence and K-segmentation strategies into PSSM, [J] Analytical Biochemistry, Volume 589, 2020, Pages 113494.

  8. Publications  2019

    1. Zar Nawab Khan Swati, Qinghua Zhao, Muhammad Kabir, Farman Ali, Zakir Ali, Saeed Ahmed, Jianfeng Lu*; Brain Tumor Classification for MR Images using Transfer Learning and Fine-Tuning, [J] Computerized Medical Imaging and Graphics, Volume 75, 2019, Pages 34-46.

    2. Farman Ali, Saeed Ahmed, Zar Nawab Khan Swati, Shahid Akbar; DP-BINDER: machine learning model for prediction of DNA-binding proteins by fusing evolutionary and physicochemical information, [J] Journal of Computer-Aided Molecular Designs, Volume 33, 2019, Pages 645-658.

    3. SM Hasan Mahmud, Wenyu Chen, Hosney Jahan, Yongsheng Liu, Nasir Islam Sujan, Saeed Ahmed; iDTi-CSsmoteB: identification of drug–target interaction based on drug chemical structure and protein sequence using XGBoost with over-sampling technique SMOTE, [J] IEEE Access, Volume 7, 2019, Pages 48699-48714.

    4. Zar Nawab Khan Swati, Qinghua Zhao, Muhammad Kabir, Farman Ali, Zakir Ali, Saeed Ahmed, Jianfeng Lu*; Content-Based Brain Tumor Retrieval for MR Images Using Transfer Learning, [J] IEEE Access, Volume 7, Issue 1, 2019, Pages 17809-17822.

    5. Muhammad Kabir, Muhammad Arif, Farman Ali, Saeed Ahmad, Zar Nawab Khan Swati, Dong-Jun Yu*; Prediction of membrane protein types by exploring local discriminative information from evolutionary profiles, [J] Analytical Biochemistry, Volume 564-565, 2019, Pages 123-132.

  9. Publications  2018

    1. Saeed Ahmad*, Muhammad Kabir, Zakir Ali, Muhammad Arif, Farman Ali, Dong-Jun Yu; An Integrated Feature Selection algorithm for Cancer Classification using Gene Expression Data, [J] Combinatorial Chemistry & High Throughput Screening, Volume 21, Issue 9, 2018, Pages 631-645.

    2. Saeed Ahmad*, Muhammad Kabir*, Muhammad Arif, Zakir Ali, Farman Ali, Zar Nawab Khan Swati; Improving secretory proteins prediction in Mycobacterium tuberculosis using the unbiased dipeptide composition with support vector machine, [J] International Journal of Data Mining and Bioinformatics, Volume 21, Issue 3, 2018, Pages 212-229.

    3. Muhammad Kabir, Muhammad Arif, Saeed Ahmad*, Zakir Ali, Zar Nawab Khan Swati, Dong-Jun Yu*; Intelligent computational method for discrimination of anticancer peptides by incorporating sequential and evolutionary profiles information, [J] Chemometrics and Intelligent Laboratory Systems, Volume 182, 2018, Pages 158-165.

    4. Muhammad Kabir, Saeed Ahmad, Muhammad Iqbal, Zar Nawab Khan Swati, Zi Liu, Dong-Jun Yu*; Improving prediction of extracellular matrix proteins using evolutionary information via a grey system model and asymmetric under-sampling technique, [J] Chemometrics and Intelligent Laboratory Systems, Volume 174, 2018, Pages 22-32.

  10. Publications  2017

    1. Muslim Khan, Maqsood Hayat, Sher Afzal Khan, Saeed Ahmad, Nadeem Iqbal; Bi-PSSM: Position specific scoring matrix based intelligent computational model for identification of mycobacterial membrane proteins, [J] Journal of Theoretical Biology, Volume 435, 2017, Pages 116-124.

  11. Publications  2015

    1. Muhammad Kabir, Muhammad Iqbal, Saeed Ahmad, Maqsood Hayat*; iTIS-PseKNC: Identification of Translation Initiation Site in human genes using pseudo k-tuple nucleotides composition, [J] Computers in Biology and Medicine, Volume 66, 2015, Pages 252-257.

    2. Saeed Ahmad, Muhammad Kabir, Maqsood Hayat*; Identification of Heat Shock Protein Families and J-Protein Types by incorporating Dipeptide Composition into Chou's general PseAAC, [J] Computer Methods and Programs in Biomedicine, Volume 122, 2015, Pages 165-174.

  12. Conference Papers  

    1. Adil Yousaf, Muhammad Rashid Rasheed, Muhammad Arif, Abdullah Yousafzai, Muhammad Kabir, Saeed Ahmed*; Recent advancements in predicting protein phosphorylation sites using machine learning methods, [J] 2021 International Conference on Innovative Computing (ICIC) -IEEE, 2021, Pages 1-6.

    2. Muhammad Rashid Rasheed, Mehwish Gill, Muhammad Asif Subhani, Muhammad Arif, Saeed Ahmed, Muhammd Kabir; Comprehensive analysis of machine learning based predictors for identifying DNase I hypersensitive site, [J] 2021 International Conference on Innovative Computing (ICIC) -IEEE, 2021, Pages 1-6.

    13. *Corresponding Author.

MS/PhD Thesis Supervised:

  1. Mehwish Gill  Co-Supervisor - 2022

    Prediction and analysis of computational methods for the identification of enhancers and their strength.

  2. Roha Arif  Co-Supervisor - 2023

    Identification of Tumor-Homing Peptides Using Deep features combined Support vector machine.

  3. Sameera Kanwal  Supervisor - 2023

    Prediction of Antimicrobial peptides using feature representation learning.

  4. Abdullah Muhammad Asghar  Supervisor - 2023

    Large-scale comparative review and assessment of computational methods for identification of nucleosome positioning.

  5. Farwa Arshad  Co-Supervisor - 2023

    Identification of anti-diabetic peptides using stacked based ensemble learning.

  6. Aqsa Amjad  Supervisor - 2023

    Analysis and identification of promoters and their strength based on a deep neural network with sequential features.

  7. Shumaila Kanwal  Co-Supervisor - 2023

    Prediction of Ampylation sites using protein language model with deep cascade random forest.

  8. Hina Farooq  Supervisor - 2023

    A novel approach for accurate prediction of Cyclin Proteins using stacking ensemble based learning.

  9. Muhammad Rehan Amjad  Supervisor - 2023

    Prediction of Antiviral Peptides using Long-Short-Term-Memory (LSTM) Based Convolution Neural Network .

  10. ZUBDA KHANUM  Supervisor - 2023

    Analysis on prediction of lysine malonylation sites by exploiting informative features in machine learning framework using principal component analysis.

  11. Zoha Kashaf  Supervisor - 2023

    Cell-Specific Long Non-Coding RNA Prediction Using Deep Learning Techniques.

Editorial and Reviewer Services:

  1. Editorial Services  

    Member of Editorial Board in journal &qout;BMC Bioinformatics&qout;, BMC Part of Springer Nature&qout;

  2. Review Services  

    • 1. Briefings in Bioinformatics.
    • 2. Engineering Applications of Artificial Intelligence.
    • 3. Current Opinion in Biomedical Engineering.
    • 4. Artificial Intelligence In Medicine.
    • 5. Journal of Computational Biology.
    • 6. Computers in Biology and Medicine.
    • 7. Knowledge-Based Systems.
    • 8. Information Science.
    • 9. Genomics.
    • 10. ACS Omega.
    • 11. SN Applied Sciences.
    • 12. SAR and QSAR in Environmental Research.
    • 13. IEEE Journal of Biomedical and Health Informatics.
    • 14. Visual Computing for Industry, Biomedicine, and Art.
    • 15. Journal of King Saud University - Computer and Information Sciences.
    • 16. IEEE Access.
    • 17. AI Open.
    • 18. Genes - MDPI.
    • 19. Symmetry - MDPI.
    • 20. International Conference on Innovative Computing – UMT.
    • 21. International Conference on Frontiers of Information Technology - COMSATS.
    • Bioinformatics Advances

Contact ME

saeed.ahmad075@gmail.com
+92-344-3820531
WhatsApp: +92-344-3820531

Address

Khyber Pakhtunkhwa, Swabi

Pakistan

© Copyright 2026

   

Dr. Saeed Ahmed

Developed by Dr.Saeed Ahmed