RNAG: a new Gibbs sampler for predicting RNA secondary structure for unaligned sequences. - Donglai Wei 001; Lauren V. Alpert; Charles E. Lawrence (Bioinform., 2011)

Learning Deformations with Parallel Transport. - Donglai Wei 001; Dahua Lin; John W. Fisher III (ECCV (2), 2012)

A Video Representation Using Temporal Superpixels. - Jason Chang 001; Donglai Wei 001; John W. Fisher III (CVPR, 2013)

A Data-Driven Regularization Model for Stereo and Flow. - Donglai Wei 001; Ce Liu 001; William T. Freeman (3DV, 2014)

Seeing the Arrow of Time. - Lyndsey C. Pickup; Zheng Pan; Donglai Wei 001; Yi-Chang Shih; Changshui Zhang; Andrew Zisserman; Bernhard Schölkopf; William T. Freeman (CVPR, 2014)

Understanding Intra-Class Knowledge Inside CNN. - Donglai Wei 001; Bolei Zhou; Antonio Torralba 001; William T. Freeman (CoRR, 2015)

Deviation magnification: revealing departures from ideal geometries. - Neal Wadhwa; Tali Dekel; Donglai Wei 001; Frédo Durand; William T. Freeman (ACM Trans. Graph., 2015)

Mining Visual Evolution in 21 Years of Web Design. - Ali Jahanian 002; Phillip Isola; Donglai Wei 001 (CHI Extended Abstracts, 2017)

Motion microscopy for visualizing and quantifying small motions. - Neal Wadhwa; Justin G. Chen; Jonathan B. Sellon; Donglai Wei 001; Michael Rubinstein; Roozbeh Ghaffari; Dennis M. Freeman; Oral Büyüköztürk; Pai Wang 005; Sijie Sun; Sung Hoon Kang; Katia Bertoldi; et al. (Proc. Natl. Acad. Sci. USA, 2017)

Discovering physics and design trends from visual temporal structures. - Donglai Wei 001 (2017)

Parallel Separable 3D Convolution for Video and Volumetric Data Understanding. - Felix Gonda; Donglai Wei 001; Toufiq Parag; Hanspeter Pfister (BMVC, 2018)

Learning and Using the Arrow of Time. - Donglai Wei 001; Joseph J. Lim; Andrew Zisserman; William T. Freeman (CVPR, 2018)

Detecting Synapse Location and Connectivity by Signed Proximity Estimation and Pruning with Deep Nets. - Toufiq Parag; Daniel R. Berger; Lee Kamentsky; Benedikt Staffler; Donglai Wei 001; Moritz Helmstaedter; Jeff W. Lichtman; Hanspeter Pfister (ECCV Workshops (6), 2018)

Biologically-Constrained Graphs for Global Connectomics Reconstruction. - Brian Matejek; Daniel Haehn; Haidong Zhu; Donglai Wei 001; Toufiq Parag; Hanspeter Pfister (CVPR, 2019)

Synapse-Aware Skeleton Generation for Neural Circuits. - Brian Matejek; Donglai Wei 001; Xueying Wang 002; Jinglin Zhao; Kálmán Palágyi; Hanspeter Pfister (MICCAI (1), 2019)

Video Enhancement with Task-Oriented Flow. - Tianfan Xue; Baian Chen; Jiajun Wu 001; Donglai Wei 001; William T. Freeman (Int. J. Comput. Vis., 2019)

A Topological Nomenclature for 3D Shape Analysis in Connectomics. - Abhimanyu Talwar; Zudi Lin; Donglai Wei 001; Yuesong Wu; Bowen Zheng; Jinglin Zhao; Won-Dong Jang; Xueying Wang 002; Jeff Lichtman; Hanspeter Pfister (CVPR Workshops, 2020)

Super-BPD: Super Boundary-to-Pixel Direction for Fast Image Segmentation. - Jianqiang Wan; Yang Liu 271; Donglai Wei 001; Xiang Bai; Yongchao Xu (CVPR, 2020)

Two Stream Active Query Suggestion for Active Learning in Connectomics. - Zudi Lin; Donglai Wei 001; Won-Dong Jang; Siyan Zhou; Xupeng Chen; Xueying Wang 002; Richard Schalek; Daniel R. Berger; Brian Matejek; Lee Kamentsky; Adi Suissa-Peleg; Daniel Haehn; et al. (ECCV (18), 2020)

Automated Measurements of Key Morphological Features of Human Embryos for IVF. - Brian D. Leahy; Won-Dong Jang; Helen Y. Yang; Robbert Struyven; Donglai Wei 001; Zhe Sun; Kylie R. Lee; Charlotte Royston; Liz Cam; Yael Kalma; Foad Azem; Dalit Ben-Yosef; et al. (MICCAI (5), 2020)

Channel Embedding for Informative Protein Identification from Highly Multiplexed Images. - Salma Abdel Magid; Won-Dong Jang; Denis Schapiro; Donglai Wei 001; James Tompkin 001; Peter K. Sorger; Hanspeter Pfister (MICCAI (5), 2020)

MitoEM Dataset: Large-Scale 3D Mitochondria Instance Segmentation from EM Images. - Donglai Wei 001; Zudi Lin; Daniel Franco-Barranco; Nils Wendt; Xingyu Liu; Wenjie Yin; Xin Huang; Aarush Gupta; Won-Dong Jang; Xueying Wang 002; Ignacio Arganda-Carreras; Jeff W. Lichtman; et al. (MICCAI (5), 2020)

Dynamic High-Pass Filtering and Multi-Spectral Attention for Image Super-Resolution. - Salma Abdel Magid; Yulun Zhang 001; Donglai Wei 001; Won-Dong Jang; Zudi Lin; Yun Fu 001; Hanspeter Pfister (ICCV, 2021)

Context Reasoning Attention Network for Image Super-Resolution. - Yulun Zhang 001; Donglai Wei 001; Can Qin; Huan Wang 014; Hanspeter Pfister; Yun Fu 001 (ICCV, 2021)

Consistent Recurrent Neural Networks For 3d Neuron Segmentation. - Felix Gonda; Donglai Wei 001; Hanspeter Pfister (ISBI, 2021)

NucMM Dataset: 3D Neuronal Nuclei Instance Segmentation at Sub-Cubic Millimeter Scale. - Zudi Lin; Donglai Wei 001; Mariela D. Petkova; Yuelong Wu; Zergham Ahmed; Krishna Swaroop K; Silin Zou; Nils Wendt; Jonathan Boulanger-Weill; Xueying Wang 002; Nagaraju Dhanyasi; Ignacio Arganda-Carreras; et al. (MICCAI (1), 2021)

Developmental Stage Classification of Embryos Using Two-Stream Neural Network with Linear-Chain Conditional Random Field. - Stanislav Lukyanenko; Won-Dong Jang; Donglai Wei 001; Robbert Struyven; Yoon Kim; Brian D. Leahy; Helen Y. Yang; Alexander M. Rush; Dalit Ben-Yosef; Daniel Needleman; Hanspeter Pfister (MICCAI (8), 2021)

AxonEM Dataset: 3D Axon Instance Segmentation of Brain Cortical Regions. - Donglai Wei 001; Kisuk Lee; Hanyu Li; Ran Lu; J. Alexander Bae; Zequan Liu; Lifu Zhang; Márcia dos Santos; Zudi Lin; Thomas D. Uram; Xueying Wang 002; Ignacio Arganda-Carreras; et al. (MICCAI (1), 2021)

RibSeg Dataset and Strong Point Cloud Baselines for Rib Segmentation from CT Scans. - Jiancheng Yang; Shixuan Gu; Donglai Wei 001; Hanspeter Pfister; Bingbing Ni (MICCAI (1), 2021)

Learning to Generate Realistic Noisy Images via Pixel-level Noise-aware Adversarial Training. - Yuanhao Cai; Xiaowan Hu; Haoqian Wang; Yulun Zhang 001; Hanspeter Pfister; Donglai Wei 001 (NeurIPS, 2021)

MedMNIST v2: A Large-Scale Lightweight Benchmark for 2D and 3D Biomedical Image Classification. - Jiancheng Yang; Rui Shi; Donglai Wei 001; Zequan Liu; Lin Zhao; Bilian Ke; Hanspeter Pfister; Bingbing Ni (CoRR, 2021)

Object Propagation via Inter-Frame Attentions for Temporally Stable Video Instance Segmentation. - Anirudh Srinivasan Chakravarthy; Won-Dong Jang; Zudi Lin; Donglai Wei 001; Song Bai 001; Hanspeter Pfister (CoRR, 2021)

PyTorch Connectomics: A Scalable and Flexible Segmentation Framework for EM Connectomics. - Zudi Lin; Donglai Wei 001; Jeff Lichtman; Hanspeter Pfister (CoRR, 2021)

YouMVOS: An Actor-centric Multi-shot Video Object Segmentation Dataset. - Donglai Wei 001; Siddhant Kharbanda; Sarthak Arora; Roshan Roy; Nishant Jain; Akash Palrecha; Tanav Shah; Shray Mathur; Ritik Mathur; Abhijay Kemkar; Anirudh Srinivasan Chakravarthy; Zudi Lin; et al. (CVPR, 2022)

Texture-based Error Analysis for Image Super-Resolution. - Salma Abdel Magid; Zudi Lin; Donglai Wei 001; Yulun Zhang 001; Jinjin Gu; Hanspeter Pfister (CVPR, 2022)

Revisiting RCAN: Improved Training for Image Super-Resolution. - Zudi Lin; Prateek Garg; Atmadeep Banerjee; Salma Abdel Magid; Deqing Sun; Yulun Zhang 001; Luc Van Gool; Donglai Wei 001; Hanspeter Pfister (CoRR, 2022)

Instance Segmentation of Unlabeled Modalities via Cyclic Segmentation GAN. - Leander Lauenburg; Zudi Lin; Ruihan Zhang 003; Márcia dos Santos; Siyu Huang; Ignacio Arganda-Carreras; Edward S. Boyden; Hanspeter Pfister; Donglai Wei 001 (CoRR, 2022)

RibSeg v2: A Large-scale Benchmark for Rib Labeling and Anatomical Centerline Extraction. - Liang Jin; Shixuan Gu; Donglai Wei 001; Kaiming Kuang; Hanspeter Pfister; Bingbing Ni; Jiancheng Yang; Ming Li 005 (CoRR, 2022)

Biomedical image analysis competitions: The state of current participation practice. - Matthias Eisenmann; Annika Reinke; Vivienn Weru; Minu Dietlinde Tizabi; Fabian Isensee; Tim J. Adler; Patrick Godau; Veronika Cheplygina; Michal Kozubek 001; Sharib Ali; Anubha Gupta; Jan Kybic; et al. (CoRR, 2022)

Scalable Biologically-Aware Skeleton Generation for Connectomic Volumes. - Brian Matejek; Tim Franzmeyer; Donglai Wei 001; Xueying Wang 002; Jinglin Zhao; Kálmán Palágyi; Jeff W. Lichtman; Hanspeter Pfister (IEEE Trans. Medical Imaging, 2022)

NucExM Dataset for Nuclei Segmentation in Expansion Microscopy. - Leander Lauenburg; Zudi Lin; Ruihan Zhang 003; Márcia dos Santos; Siyu Huang; Ignacio Arganda-Carreras; Edward S. Boyden; Hanspeter Pfister; Donglai Wei 001 (IEEE DataPort, 2022)

QuantArt: Quantizing Image Style Transfer Towards High Visual Fidelity. - Siyu Huang; Jie An 002; Donglai Wei 001; Jiebo Luo 001; Hanspeter Pfister (CVPR, 2023)

CLIPTrans: Transferring Visual Knowledge with Pre-trained Models for Multimodal Machine Translation. - Devaansh Gupta; Siddhant Kharbanda; Jiawei Zhou; Wanhua Li 001; Hanspeter Pfister; Donglai Wei 001 (ICCV, 2023)

Multi-Task Curriculum Learning for Partially Labeled Data. - Won-Dong Jang; Stanislav Lukyanenko; Donglai Wei 001; Jiancheng Yang; Brian D. Leahy; Helen Y. Yang; Dalit Ben-Yosef; Daniel Needleman; Hanspeter Pfister (ISBI, 2023)

Learning Vector Quantized Shape Code for Amodal Blastomere Instance Segmentation. - Won-Dong Jang; Donglai Wei 001; Xingxuan Zhang; Brian D. Leahy; Helen Y. Yang; James Tompkin 001; Dalit Ben-Yosef; Daniel Needleman; Hanspeter Pfister (ISBI, 2023)

High-Throughput Microscopy Image Deblurring with Graph Reasoning Attention Network. - Yulun Zhang 001; Donglai Wei 001; Richard Schalek; Yuelong Wu; Stephen G. Turney; Jeff Lichtman; Hanspeter Pfister; Yun Fu 001 (ISBI, 2023)

Structure-Preserving Instance Segmentation via Skeleton-Aware Distance Transform. - Zudi Lin; Donglai Wei 001; Aarush Gupta; Xingyu Liu; Deqing Sun; Hanspeter Pfister (MICCAI (3), 2023)

VizAbility: Multimodal Accessible Data Visualization with Keyboard Navigation and Conversational Interaction. - Joshua Gorniak; Jacob Ottiger; Donglai Wei 001; Nam Wook Kim (UIST (Adjunct Volume), 2023)

An Out-of-Domain Synapse Detection Challenge for Microwasp Brain Connectomes. - Jingpeng Wu; Yicong Li 002; Nishika Gupta; Kazunori Shinomiya; Pat Gunn; Alexey Polilov; Hanspeter Pfister; Dmitri B. Chklovskii; Donglai Wei 001 (CoRR, 2023)

The XPRESS Challenge: Xray Projectomic Reconstruction - Extracting Segmentation with Skeletons. - Tri Nguyen; Mukul Narwani; Mark Larson; Yicong Li 002; Shuhan Xie; Hanspeter Pfister; Donglai Wei 001; Nir Shavit; Lu Mi; Alexandra Pacureanu; Wei-Chung Lee 001; Aaron T. Kuan (CoRR, 2023)

The Impact of ChatGPT and LLMs on Medical Imaging Stakeholders: Perspectives and Use Cases. - Jiancheng Yang; Hongwei Bran Li; Donglai Wei 001 (CoRR, 2023)

Efficient Anatomical Labeling of Pulmonary Tree Structures via Implicit Point-Graph Networks. - Kangxian Xie; Jiancheng Yang; Donglai Wei 001; Ziqiao Weng; Pascal Fua (CoRR, 2023)

VizAbility: Multimodal Accessible Data Visualization with Keyboard Navigation and Conversational Interaction. - Joshua Gorniak; Yoon Kim; Stephen Gwon; Donglai Wei 001; Nam Wook Kim (CoRR, 2023)

3D Domain Adaptive Instance Segmentation via Cyclic Segmentation GANs. - Leander Lauenburg; Zudi Lin; Ruihan Zhang 003; Márcia dos Santos; Siyu Huang; Ignacio Arganda-Carreras; Edward S. Boyden; Hanspeter Pfister; Donglai Wei 001 (IEEE J. Biomed. Health Informatics, 2023)

Domain-Scalable Unpaired Image Translation via Latent Space Anchoring. - Siyu Huang; Jie An 002; Donglai Wei 001; Zudi Lin; Jiebo Luo 001; Hanspeter Pfister (IEEE Trans. Pattern Anal. Mach. Intell., 2023)

Current Progress and Challenges in Large-Scale 3D Mitochondria Instance Segmentation. - Daniel Franco-Barranco; Zudi Lin; Won-Dong Jang; Xueying Wang 002; Qijia Shen; Wenjie Yin; Yutian Fan; Mingxing Li 003; Chang Chen; Zhiwei Xiong; Rui Xin 003; Hao Liu; et al. (IEEE Trans. Medical Imaging, 2023)

$ mathrm R^2$-Tuning: Efficient Image-to-Video Transfer Learning for Video Temporal Grounding. - Ye Liu 002; Jixuan He; Wanhua Li 001; Junsik Kim 001; Donglai Wei 001; Hanspeter Pfister; Chang Wen Chen (ECCV (41), 2024)

Learning Socio-Temporal Graphs for Multi-Agent Trajectory Prediction. - Yuke Li; Lixiong Chen; Guangyi Chen 002; Ching-Yao Chan; Kun Zhang 001; Stefano Anzellotti; Donglai Wei 001 (HCMA@MM, 2024)

LLCP: Learning Latent Causal Processes for Reasoning-based Video Question Answer. - Guangyi Chen 002; Yuke Li; Xiao Liu; Zijian Li 001; Eman Al Suradi; Donglai Wei 001; Kun Zhang 001 (ICLR, 2024)

Learning Causal Domain-Invariant Temporal Dynamics for Few-Shot Action Recognition. - Yuke Li; Guangyi Chen 002; Ben Abramowitz; Stefano Anzellotti; Donglai Wei 001 (ICML, 2024)

S3-TTA: Scale-Style Selection for Test-Time Augmentation in Biomedical Image Segmentation. - Kangxian Xie; Siyu Huang; Sebastián Cajas Ordonez; Hanspeter Pfister; Donglai Wei 001 (ISBI, 2024)

SocialGPT: Prompting LLMs for Social Relation Reasoning via Greedy Segment Optimization. - Wanhua Li 001; Zibin Meng; Jiawei Zhou; Donglai Wei 001; Chuang Gan 001; Hanspeter Pfister (NeurIPS, 2024)

VizAbility: Enhancing Chart Accessibility with LLM-based Conversational Interaction. - Joshua Gorniak; Yoon Kim; Donglai Wei 001; Nam Wook Kim (UIST, 2024)

Two-stage error detection to improve electron microscopy image mosaicking. - Jiahao Shi; Hongyu Ge; Shuohong Wang; Donglai Wei 001; Jiancheng Yang; Ao Cheng; Richard Schalek; Jun Guo; Jeff Lichtman; Lirong Wang; Ruobing Zhang (Comput. Biol. Medicine, 2024)

TriSAM: Tri-Plane SAM for zero-shot cortical blood vessel segmentation in VEM images. - Jia Wan; Wanhua Li 001; Atmadeep Banerjee; Jason Ken Adhinarta; Evelina Sjostedt; Jingpeng Wu; Jeff Lichtman; Hanspeter Pfister; Donglai Wei 001 (CoRR, 2024)

Learning Domain-Invariant Temporal Dynamics for Few-Shot Action Recognition. - Yuke Li; Guangyi Chen 002; Ben Abramowitz; Stefano Anzellotti; Donglai Wei 001 (CoRR, 2024)

R2-Tuning: Efficient Image-to-Video Transfer Learning for Video Temporal Grounding. - Ye Liu 002; Jixuan He; Wanhua Li 001; Junsik Kim 001; Donglai Wei 001; Hanspeter Pfister; Chang Wen Chen (CoRR, 2024)

FreSeg: Frenet-Frame-based Part Segmentation for 3D Curvilinear Structures. - Shixuan Gu; Jason Ken Adhinarta; Mikhail Bessmeltsev; Jiancheng Yang; Jessica Zhang 001; Daniel R. Berger; Jeff W. Lichtman; Hanspeter Pfister; Donglai Wei 001 (CoRR, 2024)

Learning Gaze-aware Compositional GAN. - Nerea Aranjuelo; Siyu Huang; Ignacio Arganda-Carreras; Luis Unzueta; Oihana Otaegui; Hanspeter Pfister; Donglai Wei 001 (CoRR, 2024)

Affordance-Aware Object Insertion via Mask-Aware Dual Diffusion. - Jixuan He; Wanhua Li 001; Ye Liu 002; Junsik Kim 001; Donglai Wei 001; Hanspeter Pfister (CoRR, 2024)

: A Large-Scale Benchmark for Rib Labeling and Anatomical Centerline Extraction. - Liang Jin; Shixuan Gu; Donglai Wei 001; Jason Ken Adhinarta; Kaiming Kuang; Yongjie Jessica Zhang; Hanspeter Pfister; Bingbing Ni; Jiancheng Yang; Ming Li 005 (IEEE Trans. Medical Imaging, 2024)

- Visual Analysis of Neuronal Connectivity Motifs. - Jakob Troidl; Simon Warchol; Jinhan Choi; Jordan Matelsky; Nagaraju Dhanyasi; Xueying Wang 002; Brock A. Wester; Donglai Wei 001; Jeff W. Lichtman; Hanspeter Pfister; Johanna Beyer (IEEE Trans. Vis. Comput. Graph., 2024)

Learning Gaze-aware Compositional GAN from Limited Annotations. - Nerea Aranjuelo; Siyu Huang; Ignacio Arganda-Carreras; Luis Unzueta; Oihana Otaegui; Hanspeter Pfister; Donglai Wei 001 (Proc. ACM Comput. Graph. Interact. Tech., 2024)

WASPSYN: A Challenge for Domain Adaptive Synapse Detection in Microwasp Brain Connectomes. - Yicong Li 002; Wanhua Li 001; Qi Chen; Wei Huang 036; Yuda Zou; Xin Xiao; Kazunori Shinomiya; Pat Gunn; Nishika Gupta; Alexey Polilov; Yongchao Xu; Yueyi Zhang; et al. (IEEE Trans. Medical Imaging, 2024)

Efficient anatomical labeling of pulmonary tree structures via deep point-graph representation-based implicit fields. - Kangxian Xie; Jiancheng Yang; Donglai Wei 001; Ziqiao Weng; Pascal Fua (Medical Image Anal., 2025)

Deep Rib Fracture Instance Segmentation and Classification From CT on the RibFrac Challenge. - Jiancheng Yang; Rui Shi; Liang Jin; Xiaoyang Huang; Kaiming Kuang; Donglai Wei 001; Shixuan Gu; Jianying Liu; Pengfei Liu; Zhizhong Chai; Yongjie Xiao; Hao Chen 011; et al. (IEEE Trans. Medical Imaging, 2025)