S-DenseNet: A DenseNet Compression Model Based on Convolution Grouping Strategy Using Skyline Method. - Changyong Yu; Xin He; Haitao Ma; Xin Qi 004; Jiarui Lu; Yuhai Zhao (IEEE Access, 2019)

Dynamic Characteristics of Two-Mass Inertial Pipeline Robot Driven by Noncircular Gears. - Dawei Liu; Jiarui Lu (ICIRA (4), 2021)

CREAD: Combined Resolution of Ellipses and Anaphora in Dialogues. - Bo-Hsiang Tseng; Shruti Bhargava; Jiarui Lu; Joel Ruben Antony Moniz; Dhivya Piraviperumal; Lin Li; Hong Yu (NAACL-HLT, 2021)

A compositional mediation model for a binary outcome: Application to microbiome studies. - Michael B. Sohn; Jiarui Lu; Hongzhe Li (Bioinform., 2021)

KenDTI: An Ensemble Model for Predicting Drug-Target Interaction by Integrating Multi-Source Information. - Zhimiao Yu; Jiarui Lu; Yuan Jin; Yang Yang 030 (IEEE ACM Trans. Comput. Biol. Bioinform., 2021)

PEER: A Comprehensive and Multi-Task Benchmark for Protein Sequence Understanding. - Minghao Xu; Zuobai Zhang; Jiarui Lu; Zhaocheng Zhu; Yangtian Zhang; Chang Ma; Runcheng Liu; Jian Tang 005 (NeurIPS, 2022)

TorchDrug: A Powerful and Flexible Machine Learning Platform for Drug Discovery. - Zhaocheng Zhu; Chence Shi; Zuobai Zhang; Shengchao Liu; Minghao Xu; Xinyu Yuan; Yangtian Zhang; Jun-Kun Chen; Huiyu Cai; Jiarui Lu; Chang Ma; Runcheng Liu; et al. (CoRR, 2022)

ReLMole: Molecular Representation Learning Based on Two-Level Graph Similarities. - Zewei Ji; Runhan Shi; Jiarui Lu; Fang Li; Yang Yang 030 (J. Chem. Inf. Model., 2022)

STEER: Semantic Turn Extension-Expansion Recognition for Voice Assistants. - Leon Liyang Zhang; Jiarui Lu; Joel Ruben Antony Moniz; Aditya Kulkarni; Dhivya Piraviperumal; Tien Dung Tran; Nick Tzou; Hong Yu (EMNLP (Industry Track), 2023)

Protein Sequence and Structure Co-Design with Equivariant Translation. - Chence Shi; Chuanrui Wang; Jiarui Lu; Bozitao Zhong; Jian Tang 005 (ICLR, 2023)

5IDER: Unified Query Rewriting for Steering, Intent Carryover, Disfluencies, Entity Carryover and Repair. - Jiarui Lu; Bo-Hsiang Tseng; Joel Ruben Antony Moniz; Site Li; Xueyun Zhu; Hong Yu; Murat Akbacak (INTERSPEECH, 2023)

A Text-guided Protein Design Framework. - Shengchao Liu; Yutao Zhu 001; Jiarui Lu; Zhao Xu 005; Weili Nie; Anthony Gitter; Chaowei Xiao; Jian Tang 005; Hongyu Guo; Anima Anandkumar (CoRR, 2023)

Score-based Enhanced Sampling for Protein Molecular Dynamics. - Jiarui Lu; Bozitao Zhong; Jian Tang 005 (CoRR, 2023)

Intelligent Assistant Language Understanding On Device. - Cecilia Aas; Hisham Abdelsalam; Irina Belousova; Shruti Bhargava; Jianpeng Cheng 002; Robert Daland; Joris Driesen; Federico Flego; Tristan Guigue; Anders Johannsen; Partha Lal; Jiarui Lu; et al. (CoRR, 2023)

The Entity-Deduction Arena: A playground for probing the conversational reasoning and planning capabilities of LLMs. - Yizhe Zhang 002; Jiarui Lu; Navdeep Jaitly (CoRR, 2023)

Towards Foundational Models for Molecular Learning on Large-Scale Multi-Task Datasets. - Dominique Beaini; Shenyang Huang; Joao Alex Cunha; Zhiyi Li; Gabriela Moisescu-Pareja; Oleksandr Dymov; Samuel Maddrell-Mander; Callum McLean; Frederik Wenkel; Luis Müller; Jama Hussein Mohamud; Ali Parviz; et al. (CoRR, 2023)

STEER: Semantic Turn Extension-Expansion Recognition for Voice Assistants. - Leon Liyang Zhang; Jiarui Lu; Joel Ruben Antony Moniz; Aditya Kulkarni; Dhivya Piraviperumal; Tien Dung Tran; Nicholas Tzou; Hong Yu (CoRR, 2023)

MARRS: Multimodal Reference Resolution System. - Halim Cagri Ates; Shruti Bhargava; Site Li; Jiarui Lu; Siddhardha Maddula; Joel Ruben Antony Moniz; Anil Kumar Nalamalapu; Roman Hoang Nguyen; Melis Özyildirim; Alkesh Patel; Dhivya Piraviperumal; Vincent Renkens; et al. (CoRR, 2023)

Multi-modal molecule structure-text model for text-based retrieval and editing. - Shengchao Liu; Weili Nie; Chengpeng Wang; Jiarui Lu; Zhuoran Qiao; Ling Liu 001; Jian Tang 005; Chaowei Xiao; Animashree Anandkumar (Nat. Mac. Intell., 2023)

Probing the Multi-turn Planning Capabilities of LLMs via 20 Question Games. - Yizhe Zhang 002; Jiarui Lu; Navdeep Jaitly (ACL (1), 2024)

Can Large Language Models Understand Context? - Yilun Zhu 001; Joel Ruben Antony Moniz; Shruti Bhargava; Jiarui Lu; Dhivya Piraviperumal; Site Li; Yuan Zhang; Hong Yu; Bo-Hsiang Tseng (EACL (Findings), 2024)

Towards Foundational Models for Molecular Learning on Large-Scale Multi-Task Datasets. - Dominique Beaini; Shenyang Huang; Joao Alex Cunha; Zhiyi Li; Gabriela Moisescu-Pareja; Oleksandr Dymov; Samuel Maddrell-Mander; Callum McLean; Frederik Wenkel; Luis Müller; Jama Hussein Mohamud; Ali Parviz; et al. (ICLR, 2024)

Str2Str: A Score-based Framework for Zero-shot Protein Conformation Sampling. - Jiarui Lu; Bozitao Zhong; Zuobai Zhang; Jian Tang 005 (ICLR, 2024)

Study on the double-coil heat exchanger for dehumidification and heating in greenhouses: Modeling, analysis, and optimization. - Chengji Zong; He Li 023; Weitang Song; Shumei Zhao; Jiarui Lu; Qiangwei Ma (Comput. Electron. Agric., 2024)

Structure-Informed Protein Language Model. - Zuobai Zhang; Jiarui Lu; Vijil Chenthamarakshan; Aurélie C. Lozano; Payel Das; Jian Tang 005 (CoRR, 2024)

ProtIR: Iterative Refinement between Retrievers and Predictors for Protein Function Annotation. - Zuobai Zhang; Jiarui Lu; Vijil Chenthamarakshan; Aurélie C. Lozano; Payel Das; Jian Tang 005 (CoRR, 2024)

Fusing Neural and Physical: Augment Protein Conformation Sampling with Tractable Simulations. - Jiarui Lu; Zuobai Zhang; Bozitao Zhong; Chence Shi; Jian Tang 005 (CoRR, 2024)

MMIDR: Teaching Large Language Model to Interpret Multimodal Misinformation via Knowledge Distillation. - Longzheng Wang; Xiaohan Xu; Lei Zhang; Jiarui Lu; Yongxiu Xu; Hongbo Xu; Chuang Zhang (CoRR, 2024)

Apple Intelligence Foundation Language Models. - Tom Gunter; Zirui Wang; Chong Wang; Ruoming Pang; Andy Narayanan; Aonan Zhang; Bowen Zhang 002; Chen Chen 005; Chung-Cheng Chiu; David Qiu; Deepak Gopinath; Dian Ang Yap; et al. (CoRR, 2024)

ToolSandbox: A Stateful, Conversational, Interactive Evaluation Benchmark for LLM Tool Use Capabilities. - Jiarui Lu; Thomas Holleis; Yizhe Zhang 002; Bernhard Aumayer; Feng Nan; Felix Bai; Shuang Ma; Shen Ma; Mengyu Li; Guoli Yin; Zirui Wang; Ruoming Pang (CoRR, 2024)

Reaction-conditioned De Novo Enzyme Design with GENzyme. - Chenqing Hua; Jiarui Lu; Yong Liu; Odin Zhang; Jian Tang 005; Rex Ying; Wengong Jin; Guy Wolf; Doina Precup; Shuangjia Zheng (CoRR, 2024)

Unsupervised Discovery of Steerable Factors When Graph Deep Generative Models Are Entangled. - Shengchao Liu; Chengpeng Wang; Jiarui Lu; Weili Nie; Hanchen Wang 002; Zhuoxinran Li; Bolei Zhou; Jian Tang 005 (Trans. Mach. Learn. Res., 2024)

A Data Alignment Method for Network Packet Capture Based on DBSCAN. - Jiarui Lu; Qinggang Su (J. Web Eng., 2024)

Structure Language Models for Protein Conformation Generation. - Jiarui Lu; Xiaoyin Chen; Stephen Zhewen Lu; Chence Shi; Hongyu Guo; Yoshua Bengio; Jian Tang 005 (ICLR, 2025)

EilMoB: Emotion-aware Incongruity Learning and Modality Bridging Network for Multi-modal Sarcasm Detection. - Haochen Zhao; Yongxiu Xu; Xinkui Lin; Jiarui Lu; Hongbo Xu; Yubin Wang (ICMR, 2025)

ToolSandbox: A Stateful, Conversational, Interactive Evaluation Benchmark for LLM Tool Use Capabilities. - Jiarui Lu; Thomas Holleis; Yizhe Zhang 002; Bernhard Aumayer; Feng Nan; Haoping Bai; Shuang Ma; Shen Ma; Mengyu Li; Guoli Yin; Zirui Wang; Ruoming Pang (NAACL (Findings), 2025)

MMAU: A Holistic Benchmark of Agent Capabilities Across Diverse Domains. - Guoli Yin; Haoping Bai; Shuang Ma; Feng Nan; Yanchao Sun; Zhaoyang Xu; Shen Ma; Jiarui Lu; Xiang Kong; Aonan Zhang; Dian Ang Yap; Yizhe Zhang 002; et al. (NAACL (Findings), 2025)

A text-guided protein design framework. - Shengchao Liu; Yanjing Li; Zhuoxinran Li; Anthony Gitter; Yutao Zhu 001; Jiarui Lu; Zhao Xu 005; Weili Nie; Arvind Ramanathan; Chaowei Xiao; Jian Tang 005; Hongyu Guo; et al. (Nat. Mac. Intell., 2025)

Self-Evolving Curriculum for LLM Reasoning. - Xiaoyin Chen; Jiarui Lu; Minsu Kim 004; Dinghuai Zhang; Jian Tang 005; Alexandre Piché; Nicolas Gontier; Yoshua Bengio; Ehsan Kamalloo (CoRR, 2025)

Aligning Protein Conformation Ensemble Generation with Physical Feedback. - Jiarui Lu; Xiaoyin Chen; Stephen Zhewen Lu; Aurélie C. Lozano; Vijil Chenthamarakshan; Payel Das; Jian Tang 005 (CoRR, 2025)

FORT: Forward-Only Regression Training of Normalizing Flows. - Danyal Rehman; Oscar Davis; Jiarui Lu; Jian Tang 005; Michael M. Bronstein; Yoshua Bengio; Alexander Tong 001; Avishek Joey Bose (CoRR, 2025)

Measuring Scientific Capabilities of Language Models with a Systems Biology Dry Lab. - Haonan Duan 002; Stephen Zhewen Lu; Caitlin Fiona Harrigan; Nishkrit Desai; Jiarui Lu; Michal Koziarski; Leonardo Cotta; Chris J. Maddison (CoRR, 2025)

AXLearn: Modular Large Model Training on Heterogeneous Infrastructure. - Mark Lee; Tom Gunter; Chang Lan; John Peebles; Hanzhi Zhou; Kelvin Zou; Sneha Bangalore; Chung-Cheng Chiu; Nan Du; Xianzhi Du; Philipp Dufter; Ruixuan Hou; et al. (CoRR, 2025)

SimpleFold: Folding Proteins is Simpler than You Think. - Yuyang Wang; Jiarui Lu; Navdeep Jaitly; Joshua M. Susskind; Miguel Ángel Bautista 001 (CoRR, 2025)

COMPASS: A Multi-Turn Benchmark for Tool-Mediated Planning & Preference Optimization. - Tian Qin; Felix Bai; Ting-Yao Hu; Raviteja Vemulapalli; Hema Swetha Koppula; Zhiyang Xu; Bowen Jin; Mert Cemri; Jiarui Lu; Zirui Wang; Meng Cao (CoRR, 2025)

Controlling Performance and Budget of a Centralized Multi-agent LLM System with Reinforcement Learning. - Bowen Jin; TJ Collins; Donghan Yu; Mert Cemri; Shenao Zhang; Mengyu Li; Jay Tang; Tian Qin; Zhiyang Xu; Jiarui Lu; Guoli Yin; Jiawei Han 001; et al. (CoRR, 2025)