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Jingbo Zhou

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22 papers

2 author rows

AAAI Conference 2026 Conference Paper

MergeDNA: Context-Aware Genome Modeling with Dynamic Tokenization Through Token Merging

Siyuan Li
Kai Yu
Anna Wang
Zicheng Liu
Chang Yu
Jingbo Zhou
Qirong Yang
Yucheng Guo

Modeling genomic sequences faces two unsolved challenges: the information density varies widely across different regions, while there is no clearly defined minimum vocabulary unit. Relying on either four primitive bases or independently designed DNA tokenizers, existing approaches with naive masked language modeling pre-training often fail to adapt to the varying complexities of genomic sequences. Leveraging Token Merging techniques, this paper introduces a hierarchical architecture that jointly optimizes a dynamic genomic tokenizer and latent Transformers with context-aware pre-training tasks. As for network structures, the tokenization module automatically chunks adjacent bases into words by stacking multiple layers of the differentiable token merging blocks with local-window constraints, then a Latent Encoder captures the global context of these merged words by full-attention blocks. Symmetrically employing a Latent Decoder and a Local Decoder, MergeDNA learns with two pre-training tasks: Merged Token Reconstruction simultaneously trains the dynamic tokenization module and adaptively filters important tokens, while Adaptive Masked Token Modeling learns to predict these filtered tokens to capture informative contents. Extensive experiments show that MergeDNA achieves superior performance on three popular DNA benchmarks and several multi-omics tasks with fine-tuning or zero-shot evaluation, outperforming typical tokenization methods and large-scale DNA foundation models.

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AAAI Conference 2026 Conference Paper

Regressor-guided Diffusion Model for De Novo Peptide Sequencing with Explicit Mass Control

Shaorong Chen
Jingbo Zhou
Jun Xia

The discovery of novel proteins relies on sensitive protein identification, for which de novo peptide sequencing (DNPS) from mass spectra is a crucial approach. While deep learning has advanced DNPS, existing models inadequately enforce the fundamental mass consistency constraint—that a predicted peptide's mass must match the experimental measured precursor mass. Previous DNPS methods often treat this critical information as a simple input feature or use it in post-processing, leading to numerous implausible predictions that do not adhere to this fundamental physical property. To address this limitation, we introduce DiffuNovo, a novel regressor-guided diffusion model for de novo peptide sequencing that provides explicit peptide-level mass control. Our approach integrates the mass constraint at two critical stages: during training, a novel peptide-level mass loss guides model optimization, while at inference, regressor-based guidance from gradient-based updates in the latent space steers the generation to compel the predicted peptide adheres to the mass constraint. Comprehensive evaluations on established benchmarks demonstrate that DiffuNovo surpasses state-of-the-art methods in DNPS accuracy. Additionally, as the first DNPS model to employ a diffusion model as its core backbone, DiffuNovo leverages the powerful controllability of diffusion architecture and achieves a significant reduction in mass error, thereby producing much more physically plausible peptides. These innovations represent a substantial advancement toward robust and broadly applicable DNPS. The source code is available in the supplementary material.

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IJCAI Conference 2025 Conference Paper

A Comprehensive and Systematic Review for Deep Learning-Based De Novo Peptide Sequencing

Jun Xia
Jingbo Zhou
Shaorong Chen
Tianze Ling
Stan Z. Li

Tandem mass spectrometry (MS/MS) has revolutionized the field of proteomics, enabling the high-throughput identification of proteins. However, one of the central challenges in mass spectrometry-based proteomics remains peptide identification, especially in the absence of a comprehensive peptide database. While traditional database search methods compare observed mass spectra to pre-existing protein databases, they are limited by the availability and completeness of these databases. \emph{De novo} peptide sequencing, which derives peptide sequences directly from mass spectra, has emerged as a crucial approach in such cases. In recent years, deep learning has made significant strides in this domain. These methods train deep neural networks for translating mass spectra into peptide sequences without relying on any pre-constructed databases. Despite significant progress, this field still lacks a comprehensive and systematic review. In this paper, we provide the first review of deep learning-based \emph{de novo} peptide sequencing techniques from the perspectives of data types, model architectures, decoding strategies, applications and evaluation metrics. We also identify key challenges and highlight promising avenues for future research, providing a valuable resource for the AI and scientific communities.

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ICLR Conference 2025 Conference Paper

Bridging the Gap between Database Search and De Novo Peptide Sequencing with SearchNovo

Jun Xia 0001
Sizhe Liu
Jingbo Zhou
Shaorong Chen
Hongxin Xiang
Zicheng Liu 0006
Yue Liu 0008
Stan Z. Li

Accurate protein identification from mass spectrometry (MS) data is fundamental to unraveling the complex roles of proteins in biological systems, with peptide sequencing being a pivotal step in this process. The two main paradigms for peptide sequencing are database search, which matches experimental spectra with peptide sequences from databases, and \emph{de novo} sequencing, which infers peptide sequences directly from MS without relying on pre-constructed database. Although database search methods are highly accurate, they are limited by their inability to identify novel, modified, or mutated peptides absent from the database. In contrast, \emph{de novo} sequencing is adept at discovering novel peptides but often struggles with missing peaks issue, further leading to lower precision. We introduce SearchNovo, a novel framework that synergistically integrates the strengths of database search and \emph{de novo} sequencing to enhance peptide sequencing. SearchNovo employs an efficient search mechanism to retrieve the most similar peptide spectrum match (PSM) from a database for each query spectrum, followed by a fusion module that utilizes the reference peptide sequence to guide the generation of the target sequence. Furthermore, we observed that dissimilar (noisy) reference peptides negatively affect model performance. To mitigate this, we constructed pseudo reference PSMs to minimize their impact. Comprehensive evaluations on multiple datasets reveal that SearchNovo significantly outperforms state-of-the-art models. Also, analysis indicates that many retrieved spectra contain missing peaks absent in the query spectra, and the retrieved reference peptides often share common fragments with the target peptides. These are key elements in the recipe for SearchNovo’s success. The code is available at: \textcolor{magenta}{\url{https://github.com/junxia97/SearchNovo}}.

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IJCAI Conference 2025 Conference Paper

GRAPE: Heterogeneous Graph Representation Learning for Genetic Perturbation with Coding and Non-Coding Biotype

Changxi Chi
Jun Xia
Jingbo Zhou
Jiabei Cheng
Chang Yu
Stan Z. Li

Predicting genetic perturbations enables the identification of potentially crucial genes prior to wet-lab experiments, significantly improving overall experimental efficiency. Since genes are the foundation of cellular life, building gene regulatory networks (GRN) is essential to understand and predict the effects of genetic perturbations. However, current methods fail to fully leverage gene-related information, and solely rely on simple evaluation metrics to construct coarse-grained GRN. More importantly, they ignore functional differences between biotypes, limiting the ability to capture potential gene interactions. In this work, we leverage pre-trained large language model and DNA sequence model to extract features from gene descriptions and DNA sequence data, respectively, which serve as the initialization for gene representations. Additionally, we introduce gene biotype information for the first time in genetic perturbation, simulating the distinct roles of genes with different biotypes in regulating cellular processes, while capturing implicit gene relationships through graph structure learning (GSL). We propose GRAPE, a heterogeneous graph neural network (HGNN) that leverages gene representations initialized with features from descriptions and sequences, models the distinct roles of genes with different biotypes, and dynamically refines the GRN through GSL. The results on publicly available datasets show that our method achieves state-of-the-art performance. The code for reproducing the results can be seen at the link: https: //github. com/ChangxiChi/GRAPE.

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AAAI Conference 2025 Conference Paper

Improving Retrieval Augmented Language Model with Self-Reasoning

Yuan Xia
Jingbo Zhou
Zhenhui Shi
Jun Chen
Haifeng Huang

The Retrieval-Augmented Language Model (RALM) has demonstrated remarkable performance on knowledge-intensive tasks by integrating external knowledge during inference, which mitigates the factual hallucinations inherited in large language models (LLMs). Despite these advancements, challenges persist in the implementation of RALMs, particularly in terms of reliability and traceability. Specifically, the irrelevant document retrieval may result in unhelpful responses or even deteriorate the performance of LLMs, while the lack of appropriate citations in outputs complicates efforts to verify the trustworthiness of the models. To this end, we propose a novel self-reasoning framework aimed at improving the reliability and traceability of RALMs, whose core idea is to leverage reasoning trajectories generated by the LLM itself. The framework involves constructing self-reasoning trajectories through three processes: a relevance-aware process, an evidence-aware selective process, and a trajectory analysis process. We evaluated our framework across four public datasets (two short-form QA datasets, one long-form QA dataset, and one fact verification dataset) to demonstrate its superiority. Our method can outperform existing state-of-the-art models and achieve performance comparable with GPT-4, using only 2,000 training samples.

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NeurIPS Conference 2025 Conference Paper

PRESCRIBE: Predicting Single-Cell Responses with Bayesian Estimation

Jiabei Cheng
Changxi Chi
Jingbo Zhou
Hongyi Xin
Jun Xia

In single-cell perturbation prediction, a central task is to forecast the effects of perturbing a gene unseen in the training data. The efficacy of such predictions depends on two factors: (1) the similarity of the target gene to those covered in the training data, which informs model (epistemic) uncertainty, and (2) the quality of the corresponding training data, which reflects data (aleatoric) uncertainty. Both factors are critical for determining the reliability of a prediction, particularly as gene perturbation is an inherently stochastic biochemical process. In this paper, we propose PRESCRIBE (PREdicting Single-Cell Response wIth Bayesian Estimation), a multivariate deep evidential regression framework designed to measure both sources of uncertainty jointly. Our analysis demonstrates that PRESCRIBE effectively estimates a confidence score for each prediction, which strongly correlates with its empirical accuracy. This capability enables the filtering of untrustworthy results, and in our experiments, it achieves steady accuracy improvements of over 3% compared to comparable baselines.

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ICLR Conference 2025 Conference Paper

ReNovo: Retrieval-Based \emph{De Novo} Mass Spectrometry Peptide Sequencing

Shaorong Chen
Jun Xia 0001
Jingbo Zhou
Lecheng Zhang
Zhangyang Gao
Bozhen Hu
Cheng Tan 0012
Wenjie Du 0003

Proteomics is the large-scale study of proteins. Tandem mass spectrometry, as the only high-throughput technique for protein sequence identification, plays a pivotal role in proteomics research. One of the long-standing challenges in this field is peptide identification, which entails determining the specific peptide (sequence of amino acids) that corresponds to each observed mass spectrum. The conventional approach involves database searching, wherein the observed mass spectrum is scored against a pre-constructed peptide database. However, the reliance on pre-existing databases limits applicability in scenarios where the peptide is absent from existing databases. Such circumstances necessitate \emph{de novo} peptide sequencing, which derives peptide sequence solely from input mass spectrum, independent of any peptide database. Despite ongoing advancements in \emph{de novo} peptide sequencing, its performance still has considerable room for improvement, which limits its application in large-scale experiments. In this study, we introduce a novel \textbf{Re}trieval-based \emph{De \textbf{Novo}} peptide sequencing methodology, termed \textbf{ReNovo}, which draws inspiration from database search methods. Specifically, by constructing a datastore from training data, ReNovo can retrieve information from the datastore during the inference stage to conduct retrieval-based inference, thereby achieving improved performance. This innovative approach enables ReNovo to effectively combine the strengths of both methods: utilizing the assistance of the datastore while also being capable of predicting novel peptides that are not present in pre-existing databases. A series of experiments have confirmed that ReNovo outperforms state-of-the-art models across multiple widely-used datasets, incurring only minor storage and time consumption, representing a significant advancement in proteomics. Supplementary materials include the code.

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TIST Journal 2025 Journal Article

Towards Predicting Urban Land Use Changes: A Dynamic Graph Alignment Perspective

Yu Fan
Xinjiang Lu
Hao Liu
Pengfei Wang
Liang Liu
Huadong Ma
Jingbo Zhou

Urban land use, intrinsically linked to people’s daily activities, undergoes continuous evolution, presenting a complex interplay that remains partially understood. To bridge this gap, our study leverages fine-grained human mobility data to predict these changes, adopting a novel approach that conceptualizes “community-level” land use shifts as a regression problem and represents citywide changes through dynamic graphs. We harness recent advancements in graph neural networks (GNNs), which, despite their success in various applications, face challenges in directly predicting land use changes due to the temporal mismatch between the slow evolution of urban land and the immediacy of human mobility data. Our research stands out by introducing a temporal skeleton for dynamic GNNs to synchronize human activity graphs with urban land use changes, a dynamic heterogeneous GNN approach for integrating diverse human activity data to capture essential temporal dependencies, and a novel algorithm powered by causal inference to elucidate the primary factors influencing land use predictions at the community level, all of which contribute to a training process informed by the generated causal graph. Empirically validated on three real-world datasets, our model demonstrates a performance leap over state-of-the-art baselines, marking a pivotal step toward understanding and predicting the dynamics of urban land use.

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NeurIPS Conference 2024 Conference Paper

AdaNovo: Towards Robust \emph{De Novo} Peptide Sequencing in Proteomics against Data Biases

Jun Xia
Shaorong Chen
Jingbo Zhou
Xiaojun Shan
Wenjie Du
Zhangyang Gao
Cheng Tan
Bozhen Hu

Tandem mass spectrometry has played a pivotal role in advancing proteomics, enabling the high-throughput analysis of protein composition in biological tissues. Despite the development of several deep learning methods for predicting amino acid sequences (peptides) responsible for generating the observed mass spectra, training data biases hinder further advancements of \emph{de novo} peptide sequencing. Firstly, prior methods struggle to identify amino acids with Post-Translational Modifications (PTMs) due to their lower frequency in training data compared to canonical amino acids, further resulting in unsatisfactory peptide sequencing performance. Secondly, various noise and missing peaks in mass spectra reduce the reliability of training data (Peptide-Spectrum Matches, PSMs). To address these challenges, we propose AdaNovo, a novel and domain knowledge-inspired framework that calculates Conditional Mutual Information (CMI) between the mass spectra and amino acids or peptides, using CMI for robust training against above biases. Extensive experiments indicate that AdaNovo outperforms previous competitors on the widely-used 9-species benchmark, meanwhile yielding 3. 6\% - 9. 4\% improvements in PTMs identification. The supplements contain the code.

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NeurIPS Conference 2024 Conference Paper

Deep Graph Neural Networks via Posteriori-Sampling-based Node-Adaptative Residual Module

Jingbo Zhou
Yixuan Du
Ruqiong Zhang
Jun Xia
Zhizhi Yu
Zelin Zang
Di Jin
Carl Yang

Graph Neural Networks (GNNs), a type of neural network that can learn from graph-structured data through neighborhood information aggregation, have shown superior performance in various downstream tasks. However, as the number of layers increases, node representations becomes indistinguishable, which is known as over-smoothing. To address this issue, many residual methods have emerged. In this paper, we focus on the over-smoothing issue and related residual methods. Firstly, we revisit over-smoothing from the perspective of overlapping neighborhood subgraphs, and based on this, we explain how residual methods can alleviate over-smoothing by integrating multiple orders neighborhood subgraphs to avoid the indistinguishability of the single high-order neighborhood subgraphs. Additionally, we reveal the drawbacks of previous residual methods, such as the lack of node adaptability and severe loss of high-order neighborhood subgraph information, and propose a \textbf{Posterior-Sampling-based, Node-Adaptive Residual module (PSNR)}. We theoretically demonstrate that PSNR can alleviate the drawbacks of previous residual methods. Furthermore, extensive experiments verify the superiority of the PSNR module in fully observed node classification and missing feature scenarios. Our codeis available at \href{https: //github. com/jingbo02/PSNR-GNN}{https: //github. com/jingbo02/PSNR-GNN}.

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AAAI Conference 2024 Conference Paper

Explainable Origin-Destination Crowd Flow Interpolation via Variational Multi-Modal Recurrent Graph Auto-Encoder

Qiang Zhou
Xinjiang Lu
Jingjing Gu
Zhe Zheng
Bo Jin
Jingbo Zhou

Origin-destination (OD) crowd flow, if more accurately inferred at a fine-grained level, has the potential to enhance the efficacy of various urban applications. While in practice for mining OD crowd flow with effect, the problem of spatially interpolating OD crowd flow occurs since the ineluctable missing values. This problem is further complicated by the inherent scarcity and noise nature of OD crowd flow data. In this paper, we propose an uncertainty-aware interpolative and explainable framework, namely UApex, for realizing reliable and trustworthy OD crowd flow interpolation. Specifically, we first design a Variational Multi-modal Recurrent Graph Auto-Encoder (VMR-GAE) for uncertainty-aware OD crowd flow interpolation. A key idea here is to formulate the problem as semi-supervised learning on directed graphs. Next, to mitigate the data scarcity, we incorporate a distribution alignment mechanism that can introduce supplementary modals into variational inference. Then, a dedicated decoder with a Poisson prior is proposed for OD crowd flow interpolation. Moreover, to make VMR-GAE more trustworthy, we develop an efficient and uncertainty-aware explainer that can provide explanations from the spatiotemporal topology perspective via the Shapley value. Extensive experiments on two real-world datasets validate that VMR-GAE outperforms the state-of-the-art baselines. Also, an exploratory empirical study shows that the proposed explainer can generate meaningful spatiotemporal explanations.

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NeurIPS Conference 2024 Conference Paper

NovoBench: Benchmarking Deep Learning-based \emph{De Novo} Sequencing Methods in Proteomics

Jingbo Zhou
Shaorong Chen
Jun Xia
Sizhe Sizhe Liu
Tianze Ling
Wenjie Du
Yue Liu
Jianwei Yin

Tandem mass spectrometry has played a pivotal role in advancing proteomics, enabling the analysis of protein composition in biological tissues. Many deep learning methods have been developed for \emph{de novo} peptide sequencing task, i. e. , predicting the peptide sequence for the observed mass spectrum. However, two key challenges seriously hinder the further research of this important task. Firstly, since there is no consensus for the evaluation datasets, the empirical results in different research papers are often not comparable, leading to unfair comparison. Secondly, the current methods are usually limited to amino acid-level or peptide-level precision and recall metrics. In this work, we present the first unified benchmark NovoBench for \emph{de novo} peptide sequencing, which comprises diverse mass spectrum data, integrated models, and comprehensive evaluation metrics. Recent impressive methods, including DeepNovo, PointNovo, Casanovo, InstaNovo, AdaNovo and $\pi$-HelixNovo are integrated into our framework. In addition to amino acid-level and peptide-level precision and recall, we also evaluate the models' performance in terms of identifying post-tranlational modifications (PTMs), efficiency and robustness to peptide length, noise peaks and missing fragment ratio, which are important influencing factors while seldom be considered. Leveraging this benchmark, we conduct a large-scale study of current methods, report many insightful findings that open up new possibilities for future development. The benchmark is open-sourced to facilitate future research and application. The code is available at \url{https: //github. com/Westlake-OmicsAI/NovoBench}.

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IJCAI Conference 2024 Conference Paper

Robust Reward Placement under Uncertainty

Petros Petsinis
Kaichen Zhang
Andreas Pavlogiannis
Jingbo Zhou
Panagiotis Karras

We consider a problem of placing generators of rewards to be collected by randomly moving agents in a network. In many settings, the precise mobility pattern may be one of several possible, based on parameters outside our control, such as weather conditions. The placement should be robust to this uncertainty, to gain a competent total reward across possible networks. To study such scenarios, we introduce the Robust Reward Placement problem (RRP). Agents move randomly by a Markovian Mobility Model with a predetermined set of locations whose connectivity is chosen adversarially from a known set Π of candidates. We aim to select a set of reward states within a budget that maximizes the minimum ratio, among all candidates in Π, of the collected total reward over the optimal collectable reward under the same candidate. We prove that RRP is NP-hard and inapproximable, and develop Ψ-Saturate, a pseudo-polynomial time algorithm that achieves an ϵ-additive approximation by exceeding the budget constraint by a factor that scales as O(ln |Π|/ϵ). In addition, we present several heuristics, most prominently one inspired by a dynamic programming algorithm for the max–min 0–1 KNAPSACK problem. We corroborate our theoretical analysis with an experimental evaluation on synthetic and real data.

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AAAI Conference 2023 Conference Paper

Human-Instructed Deep Hierarchical Generative Learning for Automated Urban Planning

Dongjie Wang
Lingfei Wu
Denghui Zhang
Jingbo Zhou
Leilei Sun
Yanjie Fu

The essential task of urban planning is to generate the optimal land-use configuration of a target area. However, traditional urban planning is time-consuming and labor-intensive. Deep generative learning gives us hope that we can automate this planning process and come up with the ideal urban plans. While remarkable achievements have been obtained, they have exhibited limitations in lacking awareness of: 1) the hierarchical dependencies between functional zones and spatial grids; 2) the peer dependencies among functional zones; and 3) human regulations to ensure the usability of generated configurations. To address these limitations, we develop a novel human-instructed deep hierarchical generative model. We rethink the urban planning generative task from a unique functionality perspective, where we summarize planning requirements into different functionality projections for better urban plan generation. To this end, we develop a three-stage generation process from a target area to zones to grids. The first stage is to label the grids of a target area with latent functionalities to discover functional zones. The second stage is to perceive the planning requirements to form urban functionality projections. We propose a novel module: functionalizer to project the embedding of human instructions and geospatial contexts to the zone-level plan to obtain such projections. Each projection includes the information of land-use portfolios and the structural dependencies across spatial grids in terms of a specific urban function. The third stage is to leverage multi-attentions to model the zone-zone peer dependencies of the functionality projections to generate grid-level land-use configurations. Finally, we present extensive experiments to demonstrate the effectiveness of our framework.

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AAAI Conference 2022 Conference Paper

Efficient Device Scheduling with Multi-Job Federated Learning

Chendi Zhou
Ji Liu
Juncheng Jia
Jingbo Zhou
Yang Zhou
Huaiyu Dai
Dejing Dou

Recent years have witnessed a large amount of decentralized data in multiple (edge) devices of end-users, while the aggregation of the decentralized data remains difficult for machine learning jobs due to laws or regulations. Federated Learning (FL) emerges as an effective approach to handling decentralized data without sharing the sensitive raw data, while collaboratively training global machine learning models. The servers in FL need to select (and schedule) devices during the training process. However, the scheduling of devices for multiple jobs with FL remains a critical and open problem. In this paper, we propose a novel multi-job FL framework to enable the parallel training process of multiple jobs. The framework consists of a system model and two scheduling methods. In the system model, we propose a parallel training process of multiple jobs, and construct a cost model based on the training time and the data fairness of various devices during the training process of diverse jobs. We propose a reinforcement learning-based method and a Bayesian optimization-based method to schedule devices for multiple jobs while minimizing the cost. We conduct extensive experimentation with multiple jobs and datasets. The experimental results show that our proposed approaches significantly outperform baseline approaches in terms of training time (up to 8. 67 times faster) and accuracy (up to 44. 6% higher).

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AAAI Conference 2022 Conference Paper

GeomGCL: Geometric Graph Contrastive Learning for Molecular Property Prediction

Shuangli Li
Jingbo Zhou
Tong Xu
Dejing Dou
Hui Xiong

Recently many efforts have been devoted to applying graph neural networks (GNNs) to molecular property prediction which is a fundamental task for computational drug and material discovery. One of major obstacles to hinder the successful prediction of molecular property by GNNs is the scarcity of labeled data. Though graph contrastive learning (GCL) methods have achieved extraordinary performance with insufficient labeled data, most focused on designing data augmentation schemes for general graphs. However, the fundamental property of a molecule could be altered with the augmentation method (like random perturbation) on molecular graphs. Whereas, the critical geometric information of molecules remains rarely explored under the current GNN and GCL architectures. To this end, we propose a novel graph contrastive learning method utilizing the geometry of the molecule across 2D and 3D views, which is named GeomGCL. Specifically, we first devise a dual-view geometric message passing network (GeomMPNN) to adaptively leverage the rich information of both 2D and 3D graphs of a molecule. The incorporation of geometric properties at different levels can greatly facilitate the molecular representation learning. Then a novel geometric graph contrastive scheme is designed to make both geometric views collaboratively supervise each other to improve the generalization ability of GeomMPNN. We evaluate GeomGCL on various downstream property prediction tasks via a finetune process. Experimental results on seven real-life molecular datasets demonstrate the effectiveness of our proposed GeomGCL against state-of-the-art baselines.

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AAAI Conference 2021 Conference Paper

C-Watcher: A Framework for Early Detection of High-Risk Neighborhoods Ahead of COVID-19 Outbreak

Congxi Xiao
Jingbo Zhou
Jizhou Huang
An Zhuo
Ji Liu
Haoyi Xiong
Dejing Dou

The novel coronavirus disease (COVID-19) has crushed daily routines and is still rampaging through the world. Existing solution for nonpharmaceutical interventions usually needs to timely and precisely select a subset of residential urban areas for containment or even quarantine, where the spatial distribution of confirmed cases has been considered as a key criterion for the subset selection. While such containment measure has successfully stopped or slowed down the spread of COVID-19 in some countries, it is criticized for being inefficient or ineffective, as the statistics of confirmed cases are usually time-delayed and coarse-grained. To tackle the issues, we propose C-Watcher, a novel data-driven framework that aims at screening every neighborhood in a target city and predicting infection risks, prior to the spread of COVID-19 from epicenters to the city. In terms of design, C-Watcher collects large-scale long-term human mobility data from Baidu Maps, then characterizes every residential neighborhood in the city using a set of features based on urban mobility patterns. Furthermore, to transfer the firsthand knowledge (witted in epicenters) to the target city before local outbreaks, we adopt a novel adversarial encoder framework to learn “city-invariant” representations from the mobility-related features for precise early detection of high-risk neighborhoods, even before any confirmed cases known, in the target city. We carried out extensive experiments on C-Watcher using the real-data records in the early stage of COVID-19 outbreaks, where the results demonstrate the efficiency and effectiveness of C-Watcher for early detection of high-risk neighborhoods from a large number of cities.

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AAAI Conference 2021 Conference Paper

Tracking Interaction States for Multi-Turn Text-to-SQL Semantic Parsing

Run-Ze Wang
Zhen-Hua Ling
Jingbo Zhou
Yu Hu

The task of multi-turn text-to-SQL semantic parsing aims to translate natural language utterances in an interaction into SQL queries in order to answer them using a database which normally contains multiple table schemas. Previous studies on this task usually utilized contextual information to enrich utterance representations and to further influence the decoding process. While they ignored to describe and track the interaction states which are determined by history SQL queries and are related with the intent of current utterance. In this paper, two kinds of interaction states are defined based on schema items and SQL keywords separately. A relational graph neural network and a non-linear layer are designed to update the representations of these two states respectively. The dynamic schema-state and SQL-state representations are then utilized to decode the SQL query corresponding to current utterance. Experimental results on the challenging CoSQL dataset demonstrate the effectiveness of our proposed method, which achieves better performance than other published methods on the task leaderboard.

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AAAI Conference 2020 Conference Paper

Generative Adversarial Regularized Mutual Information Policy Gradient Framework for Automatic Diagnosis

Yuan Xia
Jingbo Zhou
Zhenhui Shi
Chao Lu
Haifeng Huang

Automatic diagnosis systems have attracted increasing attention in recent years. The reinforcement learning (RL) is an attractive technique for building an automatic diagnosis system due to its advantages for handling sequential decision making problem. However, the RL method still cannot achieve good enough prediction accuracy. In this paper, we propose a Generative Adversarial regularized Mutual information Policy gradient framework (GAMP) for automatic diagnosis which aims to make a diagnosis rapidly and accurately. We ﬁrst propose a new policy gradient framework based on the Generative Adversarial Network (GAN) to optimize the RL model for automatic diagnosis. In our framework, we take the generator of GAN as a policy network, and also use the discriminator of GAN as a part of the reward function. This generative adversarial regularized policy gradient framework can try to avoid generating randomized trials of symptom inquires deviated from the common diagnosis paradigm. In addition, we add mutual information to enhance the reward function to encourage the model to select the most discriminative symptoms to make a diagnosis. Experiment evaluations on two public datasets show that our method beats the state-of-art methods, not only can achieve higher diagnosis accuracy, but also can use a smaller number of inquires to make diagnosis decision.

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AAAI Conference 2020 Conference Paper

Semi-Supervised Hierarchical Recurrent Graph Neural Network for City-Wide Parking Availability Prediction

Weijia Zhang
Hao Liu
Yanchi Liu
Jingbo Zhou
Hui Xiong

The ability to predict city-wide parking availability is crucial for the successful development of Parking Guidance and Information (PGI) systems. Indeed, the effective prediction of city-wide parking availability can improve parking efﬁciency, help urban planning, and ultimately alleviate city congestion. However, it is a non-trivial task for predicting citywide parking availability because of three major challenges: 1) the non-Euclidean spatial autocorrelation among parking lots, 2) the dynamic temporal autocorrelation inside of and between parking lots, and 3) the scarcity of information about real-time parking availability obtained from real-time sensors (e. g. , camera, ultrasonic sensor, and GPS). To this end, we propose Semi-supervised Hierarchical Recurrent Graph Neural Network (SHARE) for predicting city-wide parking availability. Speciﬁcally, we ﬁrst propose a hierarchical graph convolution structure to model non-Euclidean spatial autocorrelation among parking lots. Along this line, a contextual graph convolution block and a soft clustering graph convolution block are respectively proposed to capture local and global spatial dependencies between parking lots. Additionally, we adopt a recurrent neural network to incorporate dynamic temporal dependencies of parking lots. Moreover, we propose a parking availability approximation module to estimate missing real-time parking availabilities from both spatial and temporal domain. Finally, experiments on two realworld datasets demonstrate the prediction performance of SHARE outperforms seven state-of-the-art baselines.

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AAAI Conference 2016 Conference Paper

Fusing Social Networks with Deep Learning for Volunteerism Tendency Prediction

Yongpo Jia
Xuemeng Song
Jingbo Zhou
Li Liu
Liqiang Nie
David Rosenblum

Social networks contain a wealth of useful information. In this paper, we study a challenging task for integrating users’ information from multiple heterogeneous social networks to gain a comprehensive understanding of users’ interests and behaviors. Although much effort has been dedicated to study this problem, most existing approaches adopt linear or shallow models to fuse information from multiple sources. Such approaches cannot properly capture the complex nature of and relationships among different social networks. Adopting deep learning approaches to learning a joint representation can better capture the complexity, but this neglects measuring the level of conﬁdence in each source and the consistency among different sources. In this paper, we present a framework for multiple social network learning, whose core is a novel model that fuses social networks using deep learning with source conﬁdence and consistency regularization. To evaluate the model, we apply it to predict individuals’ tendency to volunteerism. With extensive experimental evaluations, we demonstrate the effectiveness of our model, which outperforms several state-of-the-art approaches in terms of precision, recall and F1-score.

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