16S rRNA sequence embeddings: Meaningful numeric feature representations of nucleotide sequences that are convenient for downstream analyses. - Stephen Woloszynek; Zhengqiao Zhao; Jian Chen 043; Gail L. Rosen (PLoS Comput. Biol., 2019)

Label-Retrieval-Augmented Diffusion Models for Learning from Noisy Labels. - Jian Chen 043; Ruiyi Zhang 002; Tong Yu 001; Rohan Sharma; Zhiqiang Xu; Tong Sun 005; Changyou Chen (NeurIPS, 2023)

TRINS: Towards Multimodal Language Models that Can Read. - Ruiyi Zhang 002; Yanzhe Zhang; Jian Chen 043; Yufan Zhou 001; Jiuxiang Gu; Changyou Chen; Tong Sun 005 (CVPR, 2024)

TextLap: Customizing Language Models for Text-to-Layout Planning. - Jian Chen 043; Ruiyi Zhang 002; Yufan Zhou 001; Jennifer Healey; Jiuxiang Gu; Zhiqiang Xu; Changyou Chen (EMNLP (Findings), 2024)

Towards Aligned Layout Generation via Diffusion Model with Aesthetic Constraints. - Jian Chen 043; Ruiyi Zhang 002; Yufan Zhou 001; Changyou Chen (ICLR, 2024)

A probability contrastive learning framework for 3D molecular representation learning. - Jiayu Qin 001; Jian Chen 043; Rohan Sharma; Jingchen Sun; Changyou Chen (NeurIPS, 2024)

LLaVA-Read: Enhancing Reading Ability of Multimodal Language Models. - Ruiyi Zhang 002; Yufan Zhou 001; Jian Chen 043; Jiuxiang Gu; Changyou Chen; Tong Sun 005 (CoRR, 2024)

MMR: Evaluating Reading Ability of Large Multimodal Models. - Jian Chen 043; Ruiyi Zhang 002; Yufan Zhou 001; Ryan A. Rossi; Jiuxiang Gu; Changyou Chen (CoRR, 2024)

A Survey of Small Language Models. - Chien Van Nguyen; Xuan Shen; Ryan Aponte; Yu Xia 007; Samyadeep Basu; Zhengmian Hu; Jian Chen 043; Mihir Parmar; Sasidhar Kunapuli; Joe Barrow; Junda Wu; Ashish Singh; et al. (CoRR, 2024)

LoRA-Contextualizing Adaptation of Large Multimodal Models for Long Document Understanding. - Jian Chen 043; Ruiyi Zhang 002; Yufan Zhou 001; Tong Yu 001; Franck Dernoncourt; Jiuxiang Gu; Ryan A. Rossi; Changyou Chen; Tong Sun 005 (CoRR, 2024)

GUI Agents: A Survey. - Dang Nguyen; Jian Chen 043; Yu Wang 160; Gang Wu 013; Namyong Park; Zhengmian Hu; Hanjia Lyu; Junda Wu; Ryan Aponte; Yu Xia 007; Xintong Li 001; Jing Shi 005; et al. (CoRR, 2024)

GUI Agents: A Survey. - Dang Nguyen; Jian Chen 043; Yu Wang 160; Gang Wu 013; Namyong Park; Zhengmian Hu; Hanjia Lyu; Junda Wu; Ryan Aponte; Yu Xia 007; Xintong Li 001; Jing Shi 005; et al. (ACL (Findings), 2025)

SV-RAG: LoRA-Contextualizing Adaptation of MLLMs for Long Document Understanding. - Jian Chen 043; Ruiyi Zhang 002; Yufan Zhou 001; Tong Yu 001; Franck Dernoncourt; Jiuxiang Gu; Ryan A. Rossi; Changyou Chen; Tong Sun 005 (ICLR, 2025)

Towards Visual Text Grounding of Multimodal Large Language Model. - Ming Li; Ruiyi Zhang 002; Jian Chen 043; Jiuxiang Gu; Yufan Zhou 001; Franck Dernoncourt; Wanrong Zhu; Tianyi Zhou 001; Tong Sun 005 (CoRR, 2025)

Multimodal LLMs as Customized Reward Models for Text-to-Image Generation. - Shijie Zhou; Ruiyi Zhang 002; Huaisheng Zhu; Branislav Kveton; Yufan Zhou 001; Jiuxiang Gu; Jian Chen 043; Changyou Chen (CoRR, 2025)