Publications

Software Engineering

A. Dhakal

ISBN: 978-9-937-0-3279-7

Undergraduate coursebook on software engineering, covering key methodologies, system design, design patterns, project management, testing and quality assurance, and best practices for developing high-quality, scalable software solutions. Adopted by multiple universities in Nepal as a reference and teaching resource for Computer Engineering and Information Technology courses.

Diversity and Immigrants' Dream in America

K. Kandel and A. Dhakal

ISBN: 979-8-218-20375-7

A thought-provoking analysis on the challenges faced by immigrants, refugees, and international students while highlighting their social, cultural, and economic contributions to American society through policy perspectives, real-life narratives. This book analyses case studies on integration and the pursuit of the American dream while highlighting their social, cultural, and economic contributions to American society.

CryoTransformer: A Transformer Model for Picking Protein Particles from Cryo-EM Micrographs

A. Dhakal, R. Gyawali, L. Wang, and J. Cheng

Bioinformatics, 2024

A Large Expert-Curated Cryo-EM Image Dataset for Machine Learning Protein Particle Picking

A. Dhakal, R. Gyawali, L. Wang, and J. Cheng

Nature Scientific Data, 2023

Artificial intelligence in cryo-EM protein particle picking: recent advances and remaining challenges

A. Dhakal, R. Gyawali, L. Wang, and J. Cheng

Briefings in Bioinformatics, 2025

Artificial Intelligence in the Prediction of Protein-Ligand Interactions: Recent Advances and Future Directions

A. Dhakal, C. Mckay, J. Tanner, J. Cheng

Briefings in Bioinformatics, 2021

Multimodal deep learning integration of cryo-EM and AlphaFold3 for high-accuracy protein structure determination

R. Gyawali, A. Dhakal, J. Cheng

Nature Communications Chemistry, 2025

CryoSegNet: accurate cryo-EM protein particle picking by integrating the foundational AI image segmentation model and attention-gated U-Net

R. Gyawali, A. Dhakal, L. Wang, and J. Cheng

Briefings in Bioinformatics, 2024

CryoVirusDB: a labeled cryo-EM image dataset for AI-driven virus particle picking

R. Gyawali, A. Dhakal, L. Wang, and J. Cheng

bioRxiv, 2023

Predicting protein-ligand binding structure using E (n) Equivariant graph neural networks

A. Dhakal, R. Gyawali, and J. Cheng

bioRxiv, 2023

Detection and Classification of Diabetic Retinopathy Using Adaptive Boosting and Artificial Neural Network

A. Dhakal, L. P. Bastola, S. Shakya

International Journal of Advanced Research and Publications, 2019

Deep learning prediction of severe health risks for pediatric covid-19 patients with a large feature set in 2021 barda data challenge

S. Mahmud, E. Soltanikazemi, F. Boadu, A. Dhakal, J. Cheng

ArXiv, 2022

CryoFSL: an annotation-efficient, few-shot learning framework for robust protein particle picking in cryo-EM micrographs

B. Poudel, R. Gyawali, A. Dhakal, J. Cheng, D. Xu

bioRxiv, 2025

Exploring Deep Learning in Semantic Question Matching

A. Dhakal, A. Poudel, S. Pandey, S. Gaire, H. P. Baral

2018 IEEE 3rd International Conference on Computing, Communication and Security (ICCCS 2018), Kathmandu, Nepal

Image-Based Plant Disease Detection using Machine Learning

A. Dhakal, S. Pandey, S. Aryal

Science, Information and Technology National Youth Conference 2018 (SITNYC 2018), Kathmandu, Nepal

Real-Time Helmet Violation Detection in AI City Challenge 2023 with Genetic Algorithm-Enhanced YOLOv5

E. Soltanikazemi, A. Dhakal, B. Hatuwal, E. Toubal, A. Aboah, K. Palaniappan

IEEE Applied Imagery Pattern Recognition Workshop (AIPR 2023), St. Louis, USA

Adapting segment anything model (SAM) through prompt-based learning for enhanced protein identification in cryo-EM micrographs

F. He, Z. Yang, M. Gao, B. Poudel, N. Dhas, R. Gyawali, A. Dhakal, J. Cheng, D. Xu

2024 IEEE International Conference on Medical Artificial Intelligence (MedAI), Shanghai, China