Boqi Chen

boqi_profile.png

PhD Student


ETH Zurich

I’m a PhD student in Computer Science at , supervised by Prof. Gunnar Rätsch and Prof. Ender Konukoglu. I am also a Doctoral Fellow at ETH AI Center.

My research interests include (multimodal) LLM agents, world models, and AI for healthcare. Recently, I have been working on (multimodal) LLMs and LLM agents, including sequential decision-making in complex action spaces EMNLP ‘26, multimodal LLM decoding EMNLP ‘26, and multimodal reasoning over heterogeneous evidence ACL ‘26. I have also worked on 3D reconstruction ICLR ‘26 and world models ECCV ‘26.

I earned an MSc from , where I worked with Prof. Guillaume Jaume and Dr. Pushpak Pati on weakly-supervised learning and continual learning. I was a research intern at and . Besides research, I enjoy baking 🍞, traveling ✈️ and swimming 🏊‍♂️.

🎓 Work with me

I’m happy to hear from motivated students at ETH Zurich interested in a semester project or Master’s thesis. Current directions include LLM continual pretraining and post-training, LLM agents, and their applications in healthcare. If this sounds interesting, please email me with your CV, transcript, and a short note on what you’d like to work on.

News

  • [Aug, 2026] Two first-authored papers are accepted by EMNLP 2026 (Main). GPAgentBench-2K for benchmarking LLM agents on sequential decision-making in a complex action space. Revisiting Greedy Decoding for VQA for rethinking multimodal LLM decoding from a calibration perspective.
  • [Jun, 2026] My co-first-authored paper Controllable Egocentric Video Generation via Occlusion-Aware Sparse 3D Hand Joints is accepted by ECCV 2026. It generates egocentric videos controlled by sparse 3D hand joints and transfers to robotic hands.
  • [Apr, 2026] My first-authored paper MEDSYN is accepted by ACL 2026 Findings. It benchmarks how multimodal LLMs synthesize heterogeneous evidence in complex cases.
  • [Jan, 2026] I joined Apple in Shanghai as a Machine Learning & AI Engineer Intern, working on LLM agents for failure analysis.
  • [Jan, 2026] My co-authored paper YoNoSplat is accepted by ICLR 2026. It is a single feedforward model for 3D Gaussian Splatting from posed or unposed images.
  • [May, 2025] My first-authored paper Revisiting Automatic Data Curation for Vision Foundation Models in Digital Pathology is early accepted by MICCAI 2025 (top 9%). It curates web-scale data for foundation model pretraining.
  • [Oct, 2024] My first-authored paper ICMSeg is accepted by WACV 2025 for single-source cross-modality medical image segmentation via invariant causal mechanisms.
  • [Jun, 2023] I started my PhD in Computer Science at ETH Zurich as an ETH AI Center Doctoral Fellow.
  • [Jul, 2022] My co-first-authored paper ZoomMIL is accepted by ECCV 2022. It learns differentiable zooming for multiple instance learning on whole-slide images.
  • [Sep, 2021] I joined IBM Research Zurich as a research intern in the Accelerated Discovery & AI group.

Selected publications

  1. EMNLP
    GPAgentBench-2K: Benchmarking Large Language Model Agents in Complex Clinical Action Space
    Boqi Chen , Xudong Liu , Yunke Ao, and 2 more authors
    In Proceedings of the 2026 Conference on Empirical Methods in Natural Language Processing (EMNLP) , 2026
    AI4Healthcare LLM Agents
  2. EMNLP
    Revisiting Greedy Decoding for Visual Question Answering: A Calibration Perspective
    Boqi Chen , Xudong Liu , Yunke Ao, and 1 more author
    In Proceedings of the 2026 Conference on Empirical Methods in Natural Language Processing (EMNLP) , 2026
    Multimodal LLM
  3. ECCV
    Controllable Egocentric Video Generation via Occlusion-Aware Sparse 3D Hand Joints
    Chenyangguang Zhang* , Botao Ye* , Boqi Chen*, and 4 more authors
    * Equal contribution.
    In European Conference on Computer Vision (ECCV) , 2026
    3D Vision World Model
  4. ACL
    MEDSYN: Benchmarking Multi-EviDence SYNthesis in Complex Clinical Cases for Multimodal Large Language Models
    Boqi Chen , Xudong Liu , Jiachuan Peng, and 5 more authors
    In Findings of the Association for Computational Linguistics: ACL 2026 , 2026
    AI4Healthcare Multimodal LLM
  5. ICLR
    YoNoSplat: You Only Need One Model for Feedforward 3D Gaussian Splatting
    Botao Ye , Boqi Chen , Haofei Xu, and 2 more authors
    In International Conference on Learning Representations (ICLR) , 2026
    3D Vision
  6. MICCAI
    Revisiting Automatic Data Curation for Vision Foundation Models in Digital Pathology
    Boqi Chen , Cédric Vincent-Cuaz , Lydia A. Schoenpflug, and 12 more authors
    In Medical Image Computing and Computer Assisted Intervention (MICCAI) , 2025
    AI4Healthcare
  7. WACV
    Generalizable Single-Source Cross-Modality Medical Image Segmentation via Invariant Causal Mechanisms
    Boqi Chen , Yuanzhi Zhu , Yunke Ao, and 5 more authors
    In The IEEE/CVF Winter Conference on Applications of Computer Vision (WACV) , 2025
    AI4Healthcare Continual Learning
  8. ECCV
    Differentiable Zooming for Multiple Instance Learning on Whole-Slide Images
    Kevin Thandiackal* , Boqi Chen* , Pushpak Pati, and 4 more authors
    * Equal contribution.
    In European Conference on Computer Vision (ECCV) , 2022
    AI4Healthcare Weakly-Supervised Learning