Zaiqing Nie

JBHI Journal 2026 Journal Article

BioMedGPT: An Open Multimodal Large Language Model for BioMedicine

• Yizhen Luo
• Jiahuan Zhang
• Siqi Fan
• Kai Yang
• Massimo Hong
• Yushuai Wu
• Mu Qiao
• Zaiqing Nie

Recent advances in large language models (LLMs) like ChatGPT have shed light on the development of knowledgeable and versatile AI research assistants in various scientific domains. However, they fall short in biomedical applications due to a lack of proprietary biomedical knowledge and deficiencies in handling biological sequences for molecules and proteins. To address these issues, we present BioMedGPT, a multimodal large language model for assisting biomedical research. We first incorporate domain expertise into LLMs by incremental pre-training on large-scale biomedical literature. Then, we harmonize 2D molecular graphs, protein sequences, and natural language within a unified, parameter-efficient fusion architecture by fine-tuning on multimodal question-answering datasets. Through comprehensive experiments, we show that BioMedGPT performs on par with human experts in comprehending biomedical documents and answering research questions. It also exhibits promising capability in analyzing intricate functions and properties of novel molecules and proteins, surpassing state-of-the-art LLMs by 17. 1% and 49. 8% absolute gains respectively in ROUGE-L on molecule and protein question-answering.

AAAI Conference 2026 Conference Paper

StyleDrive: Towards Driving-Style Aware Benchmarking of End-To-End Autonomous Driving

• Ruiyang Hao
• Bowen Jing
• Haibao Yu
• Zaiqing Nie

Personalization, while extensively studied in conventional autonomous driving pipelines, has been largely overlooked in the context of end-to-end autonomous driving (E2EAD), despite its critical role in fostering user trust, safety perception, and real-world adoption. A primary bottleneck is the absence of large-scale real-world datasets that systematically capture driving preferences, severely limiting the development and evaluation of personalized E2EAD models. In this work, we introduce the first large-scale real-world dataset explicitly curated for personalized E2EAD, integrating comprehensive scene topology with rich dynamic context derived from agent dynamics and semantics inferred via a fine-tuned vision-language model (VLM). We propose a hybrid annotation pipeline that combines behavioral analysis, rule-and-distribution-based heuristics, and subjective semantic modeling guided by VLM reasoning, with final refinement through human-in-the-loop verification. Building upon this dataset, we introduce the first standardized benchmark for systematically evaluating personalized E2EAD models. Empirical evaluations on state-of-the-art architectures demonstrate that incorporating personalized driving preferences significantly improves behavioral alignment with human demonstrations.

AAAI Conference 2025 Conference Paper

End-to-End Autonomous Driving Through V2X Cooperation

• Haibao Yu
• Wenxian Yang
• Jiaru Zhong
• Zhenwei Yang
• Siqi Fan
• Ping Luo
• Zaiqing Nie

Cooperatively utilizing both ego-vehicle and infrastructure sensor data via V2X communication has emerged as a promising approach for advanced autonomous driving. However, current research mainly focuses on improving individual modules, rather than taking end-to-end learning to optimize final planning performance, resulting in underutilized data potential. In this paper, we introduce UniV2X, a pioneering cooperative autonomous driving framework that seamlessly integrates all key driving modules across diverse views into a unified network. We propose a sparse-dense hybrid data transmission and fusion mechanism for effective vehicle-infrastructure cooperation, offering three advantages: 1) Effective for simultaneously enhancing agent perception, online mapping, and occupancy prediction, ultimately improving planning performance. 2) Transmission-friendly for practical and limited communication conditions. 3) Reliable data fusion with interpretability of this hybrid data. We implement UniV2X, as well as reproducing several benchmark methods, on the challenging DAIR-V2X, the real-world cooperative driving dataset. Experimental results demonstrate the effectiveness of UniV2X in significantly enhancing planning performance, as well as all intermediate output performance.

ICML Conference 2025 Conference Paper

SToFM: a Multi-scale Foundation Model for Spatial Transcriptomics

• Suyuan Zhao
• Yizhen Luo
• Ganbo Yang
• Yan Zhong
• Hao Zhou 0012
• Zaiqing Nie

Spatial Transcriptomics (ST) technologies provide biologists with rich insights into single-cell biology by preserving spatial context of cells. Building foundational models for ST can significantly enhance the analysis of vast and complex data sources, unlocking new perspectives on the intricacies of biological tissues. However, modeling ST data is inherently challenging due to the need to extract multi-scale information from tissue slices containing vast numbers of cells. This process requires integrating macro-scale tissue morphology, micro-scale cellular microenvironment, and gene-scale gene expression profile. To address this challenge, we propose SToFM, a multi-scale S patial T ranscript o mics F oundation M odel. SToFM first performs multi-scale information extraction on each ST slice, to construct a set of ST sub-slices that aggregate macro-, micro- and gene-scale information. Then an SE(2) Transformer is used to obtain high-quality cell representations from the sub-slices. Additionally, we construct SToCorpus-88M, the largest high-resolution spatial transcriptomics corpus for pretraining. SToFM achieves outstanding performance on a variety of downstream tasks, such as tissue region semantic segmentation and cell type annotation, demonstrating its comprehensive understanding of ST data through capturing and integrating multi-scale information.

ICML Conference 2024 Conference Paper

ESM All-Atom: Multi-Scale Protein Language Model for Unified Molecular Modeling

• Kangjie Zheng
• Siyu Long
• Tianyu Lu
• Junwei Yang
• Xinyu Dai
• Ming Zhang 0004
• Zaiqing Nie
• Wei-Ying Ma

Protein language models have demonstrated significant potential in the field of protein engineering. However, current protein language models primarily operate at the residue scale, which limits their ability to provide information at the atom level. This limitation prevents us from fully exploiting the capabilities of protein language models for applications involving both proteins and small molecules. In this paper, we propose ESM-AA (ESM All-Atom), a novel approach that enables atom-scale and residue-scale unified molecular modeling. ESM-AA achieves this by pre-training on multi-scale code-switch protein sequences and utilizing a multi-scale position encoding to capture relationships among residues and atoms. Experimental results indicate that ESM-AA surpasses previous methods in protein-molecule tasks, demonstrating the full utilization of protein language models. Further investigations reveal that through unified molecular modeling, ESM-AA not only gains molecular knowledge but also retains its understanding of proteins.

ICML Conference 2024 Conference Paper

LangCell: Language-Cell Pre-training for Cell Identity Understanding

• Suyuan Zhao
• Jiahuan Zhang
• Yushuai Wu
• Yizhen Luo
• Zaiqing Nie

Cell identity encompasses various semantic aspects of a cell, including cell type, pathway information, disease information, and more, which are essential for biologists to gain insights into its biological characteristics. Understanding cell identity from the transcriptomic data, such as annotating cell types, has become an important task in bioinformatics. As these semantic aspects are determined by human experts, it is impossible for AI models to effectively carry out cell identity understanding tasks without the supervision signals provided by single-cell and label pairs. The single-cell pre-trained language models (PLMs) currently used for this task are trained only on a single modality, transcriptomics data, lack an understanding of cell identity knowledge. As a result, they have to be fine-tuned for downstream tasks and struggle when lacking labeled data with the desired semantic labels. To address this issue, we propose an innovative solution by constructing a unified representation of single-cell data and natural language during the pre-training phase, allowing the model to directly incorporate insights related to cell identity. More specifically, we introduce LangCell, the first Lang uage- Cell pre-training framework. LangCell utilizes texts enriched with cell identity information to gain a profound comprehension of cross-modal knowledge. Results from experiments conducted on different benchmarks show that LangCell is the only single-cell PLM that can work effectively in zero-shot cell identity understanding scenarios, and also significantly outperforms existing models in few-shot and fine-tuning cell identity understanding scenarios.

NeurIPS Conference 2024 Conference Paper

Learning Cooperative Trajectory Representations for Motion Forecasting

• Hongzhi Ruan
• Haibao Yu
• Wenxian Yang
• Siqi Fan
• Zaiqing Nie

Motion forecasting is an essential task for autonomous driving, and utilizing information from infrastructure and other vehicles can enhance forecasting capabilities. Existing research mainly focuses on leveraging single-frame cooperative information to enhance the limited perception capability of the ego vehicle, while underutilizing the motion and interaction context of traffic participants observed from cooperative devices. In this paper, we propose a forecasting-oriented representation paradigm to utilize motion and interaction features from cooperative information. Specifically, we present V2X-Graph, a representative framework to achieve interpretable and end-to-end trajectory feature fusion for cooperative motion forecasting. V2X-Graph is evaluated on V2X-Seq in vehicle-to-infrastructure (V2I) scenarios. To further evaluate on vehicle-to-everything (V2X) scenario, we construct the first real-world V2X motion forecasting dataset V2X-Traj, which contains multiple autonomous vehicles and infrastructure in every scenario. Experimental results on both V2X-Seq and V2X-Traj show the advantage of our method. We hope both V2X-Graph and V2X-Traj will benefit the further development of cooperative motion forecasting. Find the project at https: //github. com/AIR-THU/V2X-Graph.

ICML Conference 2024 Conference Paper

Mol-AE: Auto-Encoder Based Molecular Representation Learning With 3D Cloze Test Objective

• Junwei Yang
• Kangjie Zheng
• Siyu Long
• Zaiqing Nie
• Ming Zhang 0004
• Xinyu Dai
• Wei-Ying Ma
• Hao Zhou 0012

3D molecular representation learning has gained tremendous interest and achieved promising performance in various downstream tasks. A series of recent approaches follow a prevalent framework: an encoder-only model coupled with a coordinate denoising objective. However, through a series of analytical experiments, we prove that the encoder-only model with coordinate denoising objective exhibits inconsistency between pre-training and downstream objectives, as well as issues with disrupted atomic identifiers. To address these two issues, we propose Mol-AE for molecular representation learning, an auto-encoder model using positional encoding as atomic identifiers. We also propose a new training objective named 3D Cloze Test to make the model learn better atom spatial relationships from real molecular substructures. Empirical results demonstrate that Mol-AE achieves a large margin performance gain compared to the current state-of-the-art 3D molecular modeling approach.

NeurIPS Conference 2024 Conference Paper

MutaPLM: Protein Language Modeling for Mutation Explanation and Engineering

• Yizhen Luo
• Zikun Nie
• Massimo Hong
• Suyuan Zhao
• Hao Zhou
• Zaiqing Nie

Studying protein mutations within amino acid sequences holds tremendous significance in life sciences. Protein language models (PLMs) have demonstrated strong capabilities in broad biological applications. However, due to architectural design and lack of supervision, PLMs model mutations implicitly with evolutionary plausibility, which is not satisfactory to serve as explainable and engineerable tools in real-world studies. To address these issues, we present MutaPLM, a unified framework for interpreting and navigating protein mutations with protein language models. MutaPLM introduces a protein delta network that captures explicit protein mutation representations within a unified feature space, and a transfer learning pipeline with a chain-of-thought (CoT) strategy to harvest protein mutation knowledge from biomedical texts. We also construct MutaDescribe, the first large-scale protein mutation dataset with rich textual annotations, which provides cross-modal supervision signals. Through comprehensive experiments, we demonstrate that MutaPLM excels at providing human-understandable explanations for mutational effects and prioritizing novel mutations with desirable properties. Our code, model, and data are open-sourced at https: //github. com/PharMolix/MutaPLM.

ICRA Conference 2024 Conference Paper

QUEST: Query Stream for Practical Cooperative Perception

• Siqi Fan 0002
• Haibao Yu
• Wenxian Yang
• Jirui Yuan
• Zaiqing Nie

Cooperative perception can effectively enhance individual perception performance by providing additional viewpoint and expanding the sensing field. Existing cooperation paradigms are either interpretable (result cooperation) or flexible (feature cooperation). In this paper, we propose the concept of query cooperation to enable interpretable instance-level flexible feature interaction. To specifically explain the concept, we propose a cooperative perception framework, termed QUEST, which let query stream flow among agents. The cross-agent queries are interacted via fusion for co-aware instances and complementation for individual unaware instances. Taking camera-based vehicle-infrastructure perception as a typical practical application scene, the experimental results on the real-world dataset, DAIR-V2X-Seq, demonstrate the effectiveness of QUEST and further reveal the advantage of the query cooperation paradigm on transmission flexibility and robustness to packet dropout. We hope our work can further facilitate the cross-agent representation interaction for better cooperative perception in practice.

NeurIPS Conference 2023 Conference Paper

Flow-Based Feature Fusion for Vehicle-Infrastructure Cooperative 3D Object Detection

• Haibao Yu
• Yingjuan Tang
• Enze Xie
• Jilei Mao
• Ping Luo
• Zaiqing Nie

Cooperatively utilizing both ego-vehicle and infrastructure sensor data can significantly enhance autonomous driving perception abilities. However, the uncertain temporal asynchrony and limited communication conditions that are present in traffic environments can lead to fusion misalignment and constrain the exploitation of infrastructure data. To address these issues in vehicle-infrastructure cooperative 3D (VIC3D) object detection, we propose the Feature Flow Net (FFNet), a novel cooperative detection framework. FFNet is a flow-based feature fusion framework that uses a feature flow prediction module to predict future features and compensate for asynchrony. Instead of transmitting feature maps extracted from still-images, FFNet transmits feature flow, leveraging the temporal coherence of sequential infrastructure frames. Furthermore, we introduce a self-supervised training approach that enables FFNet to generate feature flow with feature prediction ability from raw infrastructure sequences. Experimental results demonstrate that our proposed method outperforms existing cooperative detection methods while only requiring about 1/100 of the transmission cost of raw data and covers all latency in one model on the DAIR-V2X dataset. The code is available https: //github. com/haibao-yu/FFNet-VIC3D.

TIST Journal 2022 Journal Article

Federated Learning for Personalized Humor Recognition

• Xu Guo
• Han Yu
• Boyang Li
• Hao Wang
• Pengwei Xing
• Siwei Feng
• Zaiqing Nie
• Chunyan Miao

Computational understanding of humor is an important topic under creative language understanding and modeling. It can play a key role in complex human-AI interactions. The challenge here is that human perception of humorous content is highly subjective. The same joke may receive different funniness ratings from different readers. This makes it highly challenging for humor recognition models to achieve personalization in practical scenarios. Existing approaches are generally designed based on the assumption that users have a consensus on whether a given text is humorous or not. Thus, they cannot handle diverse humor preferences well. In this article, we propose the FedHumor approach for the recognition of humorous content in a personalized manner through Federated Learning (FL). Extending a pre-trained language model, FedHumor guides the fine-tuning process by considering diverse distributions of humor preferences from individuals. It incorporates a diversity adaptation strategy into the FL paradigm to train a personalized humor recognition model. To the best of our knowledge, FedHumor is the first text-based personalized humor recognition model through federated learning. Extensive experiments demonstrate the advantage of FedHumor in recognizing humorous texts compared to nine state-of-the-art humor recognition approaches with superior capability for handling the diversity in humor labels produced by users with diverse preferences.

AAAI Conference 2019 Conference Paper

Learning Personalized End-to-End Goal-Oriented Dialog

• Liangchen Luo
• Wenhao Huang
• Qi Zeng
• Zaiqing Nie
• Xu Sun

Most existing works on dialog systems only consider conversation content while neglecting the personality of the user the bot is interacting with, which begets several unsolved issues. In this paper, we present a personalized end-to-end model in an attempt to leverage personalization in goal-oriented dialogs. We first introduce a PROFILE MODEL which encodes user profiles into distributed embeddings and refers to conversation history from other similar users. Then a PREFERENCE MODEL captures user preferences over knowledge base entities to handle the ambiguity in user requests. The two models are combined into the PERSONALIZED MEMN2N. Experiments show that the proposed model achieves qualitative performance improvements over state-of-the-art methods. As for human evaluation, it also outperforms other approaches in terms of task completion rate and user satisfaction.

AAAI Conference 2018 Conference Paper

CoChat: Enabling Bot and Human Collaboration for Task Completion

• Xufang Luo
• Zijia Lin
• Yunhong Wang
• Zaiqing Nie

Chatbots have drawn significant attention of late in both industry and academia. For most task completion bots in the industry, human intervention is the only means of avoiding mistakes in complex real-world cases. However, to the best of our knowledge, there is no existing research work modeling the collaboration between task completion bots and human workers. In this paper, we introduce CoChat, a dialog management framework to enable effective collaboration between bots and human workers. In CoChat, human workers can introduce new actions at any time to handle previously unseen cases. We propose a memory-enhanced hierarchical RNN (MemHRNN) to handle the one-shot learning challenges caused by instantly introducing new actions in CoChat. Extensive experiments on real-world datasets well demonstrate that CoChat can relieve most of the human workers’ workload, and get better user satisfaction rates comparing to other state-of-the-art frameworks.

AAAI Conference 2018 Conference Paper

CoLink: An Unsupervised Framework for User Identity Linkage

• Zexuan Zhong
• Yong Cao
• Mu Guo
• Zaiqing Nie

Nowadays, it is very common for one person to be in different social networks. Linking identical users across different social networks, also known as the User Identity Linkage (UIL) problem, is fundamental for many applications. There are two major challenges in the UIL problem. First, it’s extremely expensive to collect manually linked user pairs as training data. Second, the user attributes in different networks are usually defined and formatted very differently which makes attribute alignment very hard. In this paper we propose CoLink, a general unsupervised framework for the UIL problem. CoLink employs a co-training algorithm, which manipulates two independent models, the attribute-based model and the relationship-based model, and makes them reinforce each other iteratively in an unsupervised way. We also propose the sequence-to-sequence learning as a very effective implementation of the attribute-based model, which can well handle the challenge of the attribute alignment by treating it as a machine translation problem. We apply CoLink to a UIL task of mapping the employees in an enterprise network to their LinkedIn profiles. The experiment results show that CoLink generally outperforms the state-of-the-art unsupervised approaches by an F1 increase over 20%.

IJCAI Conference 2016 Conference Paper

Grounding Topic Models with Knowledge Bases

• Zhiting Hu
• Gang Luo
• Mrinmaya Sachan
• Eric Xing
• Zaiqing Nie

Topic models represent latent topics as probability distributions over words which can be hard to interpret due to the lack of grounded semantics. In this paper, we propose a structured topic representation based on an entity taxonomy from a knowledge base. A probabilistic model is developed to infer both hidden topics and entities from text corpora. Each topic is equipped with a random walk over the entity hierarchy to extract semantically grounded and coherent themes. Accurate entity modeling is achieved by leveraging rich textual features from the knowledge base. Experiments show significant superiority of our approach in topic perplexity and key entity identification, indicating potentials of the grounded modeling for semantic extraction and language understanding applications.

AAAI Conference 2014 Conference Paper

Learning Word Representation Considering Proximity and Ambiguity

• Lin Qiu
• Yong Cao
• Zaiqing Nie
• Yong Yu
• Yong Rui

Distributed representations of words (aka word embedding) have proven helpful in solving natural language processing (NLP) tasks. Training distributed representations of words with neural networks has lately been a major focus of researchers in the field. Recent work on word embedding, the Continuous Bag-of-Words (CBOW) model and the Continuous Skip-gram (Skip-gram) model, have produced particularly impressive results, significantly speeding up the training process to enable word representation learning from largescale data. However, both CBOW and Skip-gram do not pay enough attention to word proximity in terms of model or word ambiguity in terms of linguistics. In this paper, we propose Proximity-Ambiguity Sensitive (PAS) models (i. e. PAS CBOW and PAS Skip-gram) to produce high quality distributed representations of words considering both word proximity and ambiguity. From the model perspective, we introduce proximity weights as parameters to be learned in PAS CBOW and used in PAS Skip-gram. By better modeling word proximity, we reveal the strength of pooling-structured neural networks in word representation learning. The proximitysensitive pooling layer can also be applied to other neural network applications that employ pooling layers. From the linguistics perspective, we train multiple representation vectors per word. Each representation vector corresponds to a particular group of POS tags of the word. By using PAS models, we achieved a 16. 9% increase in accuracy over state-of-theart models.

JMLR Journal 2008 Journal Article

Dynamic Hierarchical Markov Random Fields for Integrated Web Data Extraction

• Jun Zhu
• Zaiqing Nie
• Bo Zhang
• Ji-Rong Wen

Existing template-independent web data extraction approaches adopt highly ineffective decoupled strategies---attempting to do data record detection and attribute labeling in two separate phases. In this paper, we propose an integrated web data extraction paradigm with hierarchical models. The proposed model is called Dynamic Hierarchical Markov Random Fields (DHMRFs). DHMRFs take structural uncertainty into consideration and define a joint distribution of both model structure and class labels. The joint distribution is an exponential family distribution. As a conditional model, DHMRFs relax the independence assumption as made in directed models. Since exact inference is intractable, a variational method is developed to learn the model's parameters and to find the MAP model structure and label assignments. We apply DHMRFs to a real-world web data extraction task. Experimental results show that: (1) integrated web data extraction models can achieve significant improvements on both record detection and attribute labeling compared to decoupled models; (2) in diverse web data extraction DHMRFs can potentially address the blocky artifact issue which is suffered by fixed-structured hierarchical models. [abs] [ pdf ][ bib ] &copy JMLR 2008. ( edit, beta )

ICML Conference 2007 Conference Paper

Dynamic hierarchical Markov random fields and their application to web data extraction

• Jun Zhu 0001
• Zaiqing Nie
• Bo Zhang 0010
• Ji-Rong Wen

ICML Conference 2005 Conference Paper

2D Conditional Random Fields for Web information extraction

• Jun Zhu 0001
• Zaiqing Nie
• Ji-Rong Wen
• Bo Zhang 0010
• Wei-Ying Ma