Publications

BM1b: Data-Efficient Scaling of Bone Marrow Foundation Models through Domain-Specific Self-Supervised Learning and Dense Morphology-Preserving Representation Learning.
Pathology Foundation Model
Nishchal Sapkota, Reyhan Kevser Keser, Yanglan Ou, Steven S. Huang, Dong Chen, Eric D. Hsi, Jansen Seheult, and Wenchao Han.
Medical Foundation Models and Benchmarks (MedFMB) Workshop, European Conference on Computer Vision (ECCV), 2026

Sparsely Supervised Surgical Video Segmentation with Reliable Asymmetric Dual Memory. (pre-release PDF)
Surgical Video Segmentation
Nishchal Sapkota, Yejia Zhang, Bofang Zheng, Xianshi Ma, Haoyan Shi, Yohannes Mariam, and Danny Z. Chen.
Medical Image Computing and Computer-Assisted Intervention (MICCAI), 2026

When Swin Transformer Meets KANs: An Improved Transformer Architecture for Medical Image Segmentation.
Task-Specific Transformer Architectures
Nishchal Sapkota, Haoyan Shi, Yejia Zhang, Xianshi Ma, Bofang Zheng, Fabian Vazquez, Pengfei Gu, Danny Z. Chen.
IEEE International Symposium on Biomedical Imaging (ISBI), 2026

H-CNN-ViT: A Hierarchical Gated Attention Multi-Branch Model for Bladder Cancer Recurrence Prediction.
Task-Specific Transformer Architectures
Xueyang Li, Zongren Wang, Yuliang Zhang, Zixuan Pan, Yu-Jen Chen, Nishchal Sapkota, Gelei Xu, Danny Z. Chen, and Yiyu Shi.
IEEE International Conference on Bioinformatics and Biomedicine (BIBM), 2025

UniCoN: Universal Conditional Networks for Multi-Age Embryonic Cartilage Segmentation with Sparsely Annotated Data.
Task-Specific Transformer Architectures
Nishchal Sapkota, Yejia Zhang, Zihao Zhao, Maria Gomez, Yuhan Hsi, Jordan A. Wilson, Kazuhiko Kawasaki, Greg Holmes, Meng Wu, Ethylin Wang Jabs, Joan T. Richtsmeier, Susan M. Motch Perrine, and Danny Z. Chen.
Nature Scientific Reports, 2025

IHCSurv: Effective Immunohistochemistry Priors for Cancer Survival Analysis in Gigapixel Multi-stain Whole Slide Images.
Computational Pathology
Yejia Zhang, Hanqing Chao, Zhongwei Qiu, Wenbin Liu, Yixuan Shen, Nishchal Sapkota, Pengfei Gu, Danny Z. Chen, Le Lu, Ke Yan, Dakai Jin, Yun Bian, and Hui Jiang.
Medical Image Computing and Computer-Assisted Intervention (MICCAI), 2024

ConUNETR: A Conditional Transformer Network for 3D Micro-CT Embryonic Cartilage Segmentation.
Task-Specific Transformer Architectures
Nishchal Sapkota, Yejia Zhang, Susan M. Motch Perrine, Yuhan Hsi, Sirui Li, Meng Wu, Greg Holmes, Abdul R. Abdulai, Ethylin W. Jabs, Joan T. Richtsmeier, and Danny Z. Chen.
IEEE International Symposium on Biomedical Imaging (ISBI), 2024

SHMC-Net: A mask-guided feature fusion network for sperm head morphology classification.
Medical Image Analysis
Nishchal Sapkota, Yejia Zhang, Sirui Li, Peixian Liang, Zhuo Zhao, Jingjing Zhang, Xiaomin Zha, Yiru Zhou, Yunxia Cao, and Danny Z. Chen.
IEEE International Symposium on Biomedical Imaging (ISBI), 2024

Boosting medical image classification with segmentation foundation model.
Medical Image Analysis
Pengfei Gu, Zihan Zhao, Hongxiao Wang, Yaopeng Peng, Yizhe Zhang, Nishchal Sapkota, and Danny Z. Chen.
IEEE International Symposium on Biomedical Imaging (ISBI), 2024

Path‐GPTOmic: A balanced multi‐modal learning framework for survival outcome prediction.
Computational Pathology
Hongxiao Wang, Yang Yang, Zhuo Zhao, Pengfei Gu, Nishchal Sapkota, and Danny Z. Chen.
IEEE International Symposium on Biomedical Imaging (ISBI), 2024

Swipe: Efficient and robust medical image segmentation with implicit patch embeddings.
Medical Image Analysis
Yejia Zhang, Pengfei Gu, Nishchal Sapkota, Yaopeng Peng, Hao Zheng, and Danny Z. Chen.
Medical Image Computing and Computer-Assisted Intervention (MICCAI), 2023

Embryonic cranial cartilage defects in the fgfr3y367c/+ mouse model of achondroplasia.
Medical Image Analysis
Susan M. Motch Perrine, Nishchal Sapkota, Kazuhiko Kawasaki, Yejia Zhang, Danny Z. Chen, Mizuho Kawasaki, Emily Durham, Yann Heuze, Laurence Legeai-Mallet, and Joan T. Richtsmeier.
Anatomical Record, 2023

A point in the right direction: Vector prediction for spatially-aware self-supervised volumetric representation learning.
Self-supervised Learning
Yejia Zhang, Pengfei Gu, Nishchal Sapkota, Hao Zheng, Peixian Liang, and Danny Z. Chen.
IEEE International Symposium on Biomedical Imaging (ISBI), 2023

Keep your friends close & enemies farther: Debiasing contrastive learning with spatial priors in 3d radiology images.
Self-supervised Learning
Yejia Zhang, Nishchal Sapkota, Pengfei Gu, Yaopeng Peng, Hao Zheng, and Danny Z. Chen.
IEEE International Conference on Bioinformatics and Biomedicine (BIBM), 2022

Unsupervised feature clustering improves contrastive representation learning for medical image segmentation.
Self-supervised Learning
Yejia Zhang, Xinrong Hu, Nishchal Sapkota, Yiyu Shi, and Danny Z. Chen.
IEEE International Conference on Bioinformatics and Biomedicine (BIBM), 2022

Probabilistic Analysis of Revenues in Online Games.
Applied Statistics and Mathematical Modeling
Nishchal Sapkota and Bernd Schroeder.
University of Southern Mississippi, 2020

Hunting Co-operation in the Middle Predator in Three Species Food Chain Model.
Applied Statistics and Mathematical Modeling
Nishchal Sapkota, Rimsha Bhatta, Phillip Dabney, and Zhifu Xie.
Proceedings of the Louisiana-Mississippi Section of the Mathematical Association of America, 2019