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Bo Zhou

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15 papers
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15

AAAI Conference 2026 Conference Paper

HiFusion: Hierarchical Intra-Spot Alignment and Regional Context Fusion for Spatial Gene Expression Prediction from Histopathology

  • Ziqiao Weng
  • Yaoyu Fang
  • Jiahe Qian
  • Xinkun Wang
  • Lee A D Cooper
  • Weidong Cai
  • Bo Zhou

Spatial transcriptomics (ST) bridges gene expression and tissue morphology but faces clinical adoption barriers due to technical complexity and prohibitive costs. While computational methods predict gene expression from H&E-stained whole-slide images (WSIs), existing approaches often fail to capture the intricate biological heterogeneity within spots and are susceptible to morphological noise when integrating contextual information from surrounding tissue. To overcome these limitations, we propose HiFusion, a novel deep learning framework that integrates two complementary components. First, we introduce the Hierarchical Intra-Spot Modeling module that extracts fine-grained morphological representations through multi-resolution sub-patch decomposition, guided by a feature alignment loss to ensure semantic consistency across scales. Concurrently, we present the Context-aware Cross-scale Fusion module, which employs cross-attention to selectively incorporate biologically relevant regional context, thereby enhancing representational capacity. This architecture enables comprehensive modeling of both cellular-level features and tissue microenvironmental cues, which are essential for accurate gene expression prediction. Extensive experiments on two benchmark ST datasets demonstrate that HiFusion achieves state-of-the-art performance across both 2D slide-wise cross-validation and more challenging 3D sample-specific scenarios. These results underscore HiFusion’s potential as a robust, accurate, and scalable solution for ST inference from routine histopathology.

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JBHI Journal 2026 Journal Article

Sparser2Sparse: Single-shot Sparser-to-Sparse Learning for Spatial Transcriptomics Imputation with Natural Image Co-learning

  • Yaoyu Fang
  • Jiahe Qian
  • Xinkun Wang
  • Lee A. Cooper
  • Bo Zhou

Spatial transcriptomics (ST) has revolutionized biomedical research by enabling high-resolution gene expression profiling within tissues. However, the high cost and scarcity of high-resolution ST data remain significant challenges. We present Single-shot Sparser-to-Sparse (S2S-ST), a novel framework for accurate ST imputation that requires only a single and low-cost sparsely sampled ST dataset alongside widely available natural images for co-training. Our approach integrates three key innovations: (1) a sparser-to-sparse self-supervised learning strategy that learns to predict partially observed sparse regions from even sparser subsets within the same sample, leveraging intrinsic spatial patterns in ST data; (2) cross-domain co-learning with natural images to enhance feature representation, and (3) a Cascaded Data Consistent Imputation Network (CDCIN) that iteratively refines predictions while preserving sampled gene data fidelity. Extensive experiments on diverse tissue types, including breast cancer, liver, and lymphoid tissue, demonstrate that our method outperforms state-of-the-art approaches in imputation accuracy. By enabling robust ST reconstruction from sparse inputs, our framework significantly reduces reliance on costly high-resolution data, facilitating potential broader adoption in biomedical research and clinical applications. Code is available at: https://github.com/Advanced-AI-in-Medicine-and-Physics-Lab/S2S-ST.

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AAAI Conference 2025 Conference Paper

Adaptive Dual Guidance Knowledge Distillation

  • Tong Li
  • Long Liu
  • Kang Liu
  • Xin Wang
  • Bo Zhou
  • Hongguang Yang
  • Kai Lu

Knowledge distillation (KD) aims to improve the performance of lightweight student networks under the guidance of pre-trained teachers. However, the large capacity gap between teachers and students limits the distillation gains. Previous methods addressing this problem have two weaknesses. First, most of them decrease the performance of pre-trained teachers, hindering students from achieving comparable performance. Second, these methods fail to dynamically adjust the transferred knowledge to be compatible with the representation ability of students, which is less effective in bridging the capacity gap. In this paper, we propose Adaptive Dual Guidance Knowledge Distillation (ADG-KD), which retains the guidance of the pre-trained teacher and uses the teacher's bidirectional optimization route guiding the student to alleviate the capacity gap problem. Specifically, ADG-KD introduces an initialized teacher, which has an identical structure to the pre-trained teacher and is optimized through the bidirectional supervision from both the pre-trained teacher and student. In this way, we construct the teacher's bidirectional optimization route to provide the students with an easy-to-hard and compatible knowledge sequence. ADG-KD trains the students under the proposed dual guidance approaches and automatically determines their importance weights, making the transferred knowledge better compatible with the representation ability of students. Extensive experiments on CIFAR-100, ImageNet, and MS-COCO demonstrate the effectiveness of our method.

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JBHI Journal 2025 Journal Article

Disentangled Representation Learning for Capturing Individualized Brain Atrophy via Pseudo-Healthy Synthesis

  • Zhuangzhuang Li
  • Kun Zhao
  • Pindong Chen
  • Dawei Wang
  • Hongxiang Yao
  • Bo Zhou
  • Jie Lu
  • Pan Wang

Brain atrophy emerges as a distinctive hallmark in various neurodegenerative diseases, demonstrating a progressive trajectory across diverse disease stages and concurrently manifesting in tandem with a discernible decline in cognitive abilities. Understanding the individualized patterns of brain atrophy is critical for precision medicine and the prognosis of neurodegenerative diseases. However, it is difficult to obtain longitudinal data to compare changes before and after the onset of diseases. In this study, we present a deep disentangled generative model (DDGM) for capturing individualized atrophy patterns via disentangling patient images into “realistic” healthy counterfactual images and abnormal residual maps. The proposed DDGM consists of four modules: normal MRI synthesis, residual map synthesis, input reconstruction module, and mutual information neural estimator (MINE). The MINE and adversarial learning strategy together ensure independence between disease-related features and features shared by both disease and healthy controls. In addition, we proposed a comprehensive evaluation of the effectiveness of synthetic pseudo-healthy images, focusing on both their healthiness and subject identity. The results indicated that the proposed DDGM effectively preserves these characteristics in the synthesized pseudo-healthy images, outperforming existing methods. The proposed method demonstrates robust generalization capabilities across two independent datasets from different races and sites. Analysis of the disease residual/saliency maps revealed specific atrophy patterns associated with Alzheimer's disease (AD), particularly in the hippocampus and amygdala regions. These accurate individualized atrophy patterns enhance the performance of AD classification tasks, resulting in an improvement in classification accuracy to 92. 50 $\pm$ 2. 70%.

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IJCAI Conference 2025 Conference Paper

Survey on Strategic Mining in Blockchain: A Reinforcement Learning Approach

  • Jichen Li
  • Lijia Xie
  • Hanting Huang
  • Bo Zhou
  • Binfeng Song
  • Wanying Zeng
  • Xiaotie Deng
  • Xiao Zhang

Strategic mining attacks, such as selfish mining, exploit blockchain consensus protocols by deviating from honest behavior to maximize rewards. Markov Decision Process (MDP) analysis faces scalability challenges in modern digital economics, including blockchain. To address these limitations, reinforcement learning (RL) provides a scalable alternative, enabling adaptive strategy optimization in complex dynamic environments. In this survey, we examine RL’s role in strategic mining analysis, comparing it to MDP-based approaches. We begin by reviewing foundational MDP models and their limitations, before exploring RL frameworks that can learn near-optimal strategies across various protocols. Building on this analysis, we compare RL techniques and their effectiveness in deriving security thresholds, such as the minimum attacker power required for profitable attacks. Expanding the discussion further, we classify consensus protocols and propose open challenges, such as multi-agent dynamics and real-world validation. This survey highlights the potential of reinforcement learning to address the challenges of selfish mining, including protocol design, threat detection, and security analysis, while offering a strategic roadmap for researchers in decentralized systems and AI-driven analytics.

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IROS Conference 2025 Conference Paper

VMTS: Vision-Assisted Teacher-Student Reinforcement Learning for Multi-Terrain Locomotion in Bipedal Robots

  • Fu Chen
  • Rui Wan
  • Peidong Liu
  • Nanxing Zheng
  • Bingyi Wang
  • Bo Zhou

Bipedal robots, due to their anthropomorphic design, offer substantial potential across various applications, yet their control is hindered by the complexity of their structure. Currently, most research focuses on proprioception-based methods, which lack the capability to overcome complex terrain. While visual perception is vital for operation in human-centric environments, its integration complicates control further. Recent reinforcement learning (RL) approaches have shown promise in enhancing legged robot locomotion, particularly with proprioception-based methods. However, terrain adaptability, especially for bipedal robots, remains a significant challenge, with most research focusing on flat-terrain scenarios. In this paper, we introduce a novel mixture of experts teacher-student network RL strategy, which enhances the performance of teacher-student policies based on visual inputs through a simple yet effective approach. Our method combines terrain selection strategies with the teacher policy, resulting in superior performance compared to traditional models. Additionally, we introduce an alignment loss between the teacher and student networks, rather than enforcing strict similarity, to improve the student’s ability to navigate diverse terrains. We validate our approach experimentally on the Limx Dynamic P1 bipedal robot, demonstrating its feasibility and robustness across multiple terrain types.

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JBHI Journal 2024 Journal Article

Brain Structural Connectivity Guided Vision Transformers for Identification of Functional Connectivity Characteristics in Preterm Neonates

  • Wei Mao
  • Yuzhong Chen
  • Zhibin He
  • Zifan Wang
  • Zhenxiang Xiao
  • Yusong Sun
  • Liang He
  • Jingchao Zhou

Preterm birth is the leading cause of death in children under five years old, and is associated with a wide sequence of complications in both short and long term. In view of rapid neurodevelopment during the neonatal period, preterm neonates may exhibit considerable functional alterations compared to term ones. However, the identified functional alterations in previous studies merely achieve moderate classification performance, while more accurate functional characteristics with satisfying discrimination ability for better diagnosis and therapeutic treatment is underexplored. To address this problem, we propose a novel brain structural connectivity (SC) guided Vision Transformer (SCG-ViT) to identify functional connectivity (FC) differences among three neonatal groups: preterm, preterm with early postnatal experience, and term. Particularly, inspired by the neuroscience-derived information, a novel patch token of SC/FC matrix is defined, and the SC matrix is then adopted as an effective mask into the ViT model to screen out input FC patch embeddings with weaker SC, and to focus on stronger ones for better classification and identification of FC differences among the three groups. The experimental results on multi-modal MRI data of 437 neonatal brains from publicly released Developing Human Connectome Project (dHCP) demonstrate that SCG-ViT achieves superior classification ability compared to baseline models, and successfully identifies holistically different FC patterns among the three groups. Moreover, these different FCs are significantly correlated with the differential gene expressions of the three groups. In summary, SCG-ViT provides a powerfully brain-guided pipeline of adopting large-scale and data-intensive deep learning models for medical imaging-based diagnosis.

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ICLR Conference 2024 Conference Paper

Learning to Solve Bilevel Programs with Binary Tender

  • Bo Zhou
  • Ruiwei Jiang
  • Siqian Shen

Bilevel programs (BPs) find a wide range of applications in fields such as energy, transportation, and machine learning. As compared to BPs with continuous (linear/convex) optimization problems in both levels, the BPs with discrete decision variables have received much less attention, largely due to the ensuing computational intractability and the incapability of gradient-based algorithms for handling discrete optimization formulations. In this paper, we develop deep learning techniques to address this challenge. Specifically, we consider a BP with binary tender, wherein the upper and lower levels are linked via binary variables. We train a neural network to approximate the optimal value of the lower-level problem, as a function of the binary tender. Then, we obtain a single-level reformulation of the BP through a mixed-integer representation of the value function. Furthermore, we conduct a comparative analysis between two types of neural networks: general neural networks and the novel input supermodular neural networks, studying their representational capacities. To solve high-dimensional BPs, we introduce an enhanced sampling method to generate higher-quality samples and implement an iterative process to refine solutions. We demonstrate the performance of these approaches through extensive numerical experiments, whose lower-level problems are linear and mixed-integer programs, respectively.

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AAAI Conference 2023 Conference Paper

Event Process Typing via Hierarchical Optimal Transport

  • Bo Zhou
  • Yubo Chen
  • Kang Liu
  • Jun Zhao

Understanding intention behind event processes in texts is important to many applications. One challenging task in this line is event process typing, which aims to tag the process with one action label and one object label describing the overall action of the process and object the process likely affects respectively. To tackle this task, existing methods mainly rely on the matching of the event process level and label level representation, which ignores two important characteristics: Process Hierarchy and Label Hierarchy. In this paper, we propose a Hierarchical Optimal Transport (HOT) method to address the above problem. Specifically, we first explicitly extract the process hierarchy and label hierarchy. Then the HOT optimally matches the two types of hierarchy. Experimental results show that our model outperforms the baseline models, illustrating the effectiveness of our model.

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IJCAI Conference 2023 Conference Paper

Latent Inspector: An Interactive Tool for Probing Neural Network Behaviors Through Arbitrary Latent Activation

  • Daniel Geißler
  • Bo Zhou
  • Paul Lukowicz

This work presents an active software instrument allowing deep learning architects to interactively inspect neural network models' output behavior from user-manipulated values in any latent layer. Latent Inspector offers multiple dimension reduction techniques to visualize the model's high dimensional latent layer output in human-perceptible, two-dimensional plots. The system is implemented with Node. js front end for interactive user input and Python back end for interacting with the model. By utilizing a general and modular architecture, our proposed solution dynamically adapts to a versatile range of models and data structures. Compared to already existing tools, our asynchronous approach of separating the training process from the inspection offers additional possibilities, such as interactive data generation, by actively working with the model instead of visualizing training logs. Overall, Latent Inspector demonstrates the possibilities as well as the appearing limits for providing a generalized, tool-based concept for enhancing model insight in terms of explainable and transparent AI.

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