Jianfeng Wu

Jianfeng Wu, Yi Su, Yanxi Chen et al.

Background: Alzheimer's Disease (AD) is the most common type of age-related dementia, affecting 6.2 million people aged 65 or older according to CDC data. It is commonly agreed that discovering an effective AD diagnosis biomarker could have enormous public health benefits, potentially preventing or delaying up to 40% of dementia cases. Tau neurofibrillary tangles are the primary driver of downstream neurodegeneration and subsequent cognitive impairment in AD, resulting in structural deformations such as hippocampal atrophy that can be observed in magnetic resonance imaging (MRI) scans. Objective: To build a surface-based model to 1) detect differences between APOE subgroups in patterns of tau deposition and hippocampal atrophy, and 2) use the extracted surface-based features to predict cognitive decline. Methods: Using data obtained from different institutions, we develop a surface-based federated Chow test model to study the synergistic effects of APOE, a previously reported significant risk factor of AD, and tau on hippocampal surface morphometry. Results: We illustrate that the APOE-specific morphometry features correlate with AD progression and better predict future AD conversion than other MRI biomarkers. For example, a strong association between atrophy and abnormal tau was identified in hippocampal subregion cornu ammonis 1 (CA1 subfield) and subiculum in e4 homozygote cohort. Conclusion: Our model allows for identifying MRI biomarkers for AD and cognitive decline prediction and may uncover a corner of the neural mechanism of the influence of APOE and tau deposition on hippocampal morphology.

Rui Ying, Mengting Hu, Jianfeng Wu et al.

Temporal knowledge graph completion aims to infer the missing facts in temporal knowledge graphs. Current approaches usually embed factual knowledge into continuous vector space and apply geometric operations to learn potential patterns in temporal knowledge graphs. However, these methods only adopt a single operation, which may have limitations in capturing the complex temporal dynamics present in temporal knowledge graphs. Therefore, we propose a simple but effective method, i.e. TCompoundE, which is specially designed with two geometric operations, including time-specific and relation-specific operations. We provide mathematical proofs to demonstrate the ability of TCompoundE to encode various relation patterns. Experimental results show that our proposed model significantly outperforms existing temporal knowledge graph embedding models. Our code is available at https://github.com/nk-ruiying/TCompoundE.

Jianfeng Wu, Yi Su, Wenhui Zhu et al.

Background: Beta-amyloid (A$β$) plaques and tau protein tangles in the brain are the defining 'A' and 'T' hallmarks of Alzheimer's disease (AD), and together with structural atrophy detectable on brain magnetic resonance imaging (MRI) scans as one of the neurodegenerative ('N') biomarkers comprise the ''ATN framework'' of AD. Current methods to detect A$β$/tau pathology include cerebrospinal fluid (CSF; invasive), positron emission tomography (PET; costly and not widely available), and blood-based biomarkers (BBBM; promising but mainly still in development). Objective: To develop a non-invasive and widely available structural MRI-based framework to quantitatively predict the amyloid and tau measurements. Methods: With MRI-based hippocampal multivariate morphometry statistics (MMS) features, we apply our Patch Analysis-based Surface Correntropy-induced Sparse coding and max-pooling (PASCS-MP) method combined with the ridge regression model to individual amyloid/tau measure prediction. Results: We evaluate our framework on amyloid PET/MRI and tau PET/MRI datasets from the Alzheimer's Disease Neuroimaging Initiative (ADNI). Each subject has one pair consisting of a PET image and MRI scan, collected at about the same time. Experimental results suggest that amyloid/tau measurements predicted with our PASCP-MP representations are closer to the real values than the measures derived from other approaches, such as hippocampal surface area, volume, and shape morphometry features based on spherical harmonics (SPHARM). Conclusion: The MMS-based PASCP-MP is an efficient tool that can bridge hippocampal atrophy with amyloid and tau pathology and thus help assess disease burden, progression, and treatment effects.

Jianfeng Wu, Sijie Mai, Haifeng Hu

Relation prediction is a task designed for knowledge graph completion which aims to predict missing relationships between entities. Recent subgraph-based models for inductive relation prediction have received increasing attention, which can predict relation for unseen entities based on the extracted subgraph surrounding the candidate triplet. However, they are not completely inductive because of their disability of predicting unseen relations. Moreover, they fail to pay sufficient attention to the role of relation as they only depend on the model to learn parameterized relation embedding, which leads to inaccurate prediction on long-tail relations. In this paper, we introduce Relation-dependent Contrastive Learning (ReCoLe) for inductive relation prediction, which adapts contrastive learning with a novel sampling method based on clustering algorithm to enhance the role of relation and improve the generalization ability to unseen relations. Instead of directly learning embedding for relations, ReCoLe allocates a pre-trained GNN-based encoder to each relation to strengthen the influence of relation. The GNN-based encoder is optimized by contrastive learning, which ensures satisfactory performance on long-tail relations. In addition, the cluster sampling method equips ReCoLe with the ability to handle both unseen relations and entities. Experimental results suggest that ReCoLe outperforms state-of-the-art methods on commonly used inductive datasets.

Zhenyuan Liu, Tong Jia, Xingyu Xing et al.

Autonomous vehicles are exposed to various weather during operation, which is likely to trigger the performance limitations of the perception system, leading to the safety of the intended functionality (SOTIF) problems. To efficiently generate data for testing the performance of visual perception algorithms under various weather conditions, a hierarchical-level rain image generative model, rain conditional CycleGAN (RCCycleGAN), is constructed. RCCycleGAN is based on the generative adversarial network (GAN) and can generate images of light, medium, and heavy rain. Different rain intensities are introduced as labels in conditional GAN (CGAN). Meanwhile, the model structure is optimized and the training strategy is adjusted to alleviate the problem of mode collapse. In addition, natural rain images of different intensities are collected and processed for model training and validation. Compared with the two baseline models, CycleGAN and DerainCycleGAN, the peak signal-to-noise ratio (PSNR) of RCCycleGAN on the test dataset is improved by 2.58 dB and 0.74 dB, and the structural similarity (SSIM) is improved by 18% and 8%, respectively. The ablation experiments are also carried out to validate the effectiveness of the model tuning.

Shengyi Hua, Jianfeng Wu, Tianle Shen et al.

Recent pathological foundation models have substantially advanced visual representation learning and multimodal interaction. However, most models still rely on a static inference paradigm in which whole-slide images are processed once to produce predictions, without reassessment or targeted evidence acquisition under ambiguous diagnoses. This contrasts with clinical diagnostic workflows that refine hypotheses through repeated slide observations and further examination requests. We propose PathFound, an agentic multimodal model designed to support evidence-seeking inference in pathological diagnosis. PathFound integrates the power of pathological visual foundation models, vision-language models, and reasoning models trained with reinforcement learning to perform proactive information acquisition and diagnosis refinement by progressing through the initial diagnosis, evidence-seeking, and final decision stages. Across several large multimodal models, adopting this strategy consistently improves diagnostic accuracy, indicating the effectiveness of evidence-seeking workflows in computational pathology. Among these models, PathFound achieves state-of-the-art diagnostic performance across diverse clinical scenarios and demonstrates strong potential to discover subtle details, such as nuclear features and local invasions.

Fang Yan, Jianfeng Wu, Jiawen Li et al.

The complexity and variability inherent in high-resolution pathological images present significant challenges in computational pathology. While pathology foundation models leveraging AI have catalyzed transformative advancements, their development demands large-scale datasets, considerable storage capacity, and substantial computational resources. Furthermore, ensuring their clinical applicability and generalizability requires rigorous validation across a broad spectrum of clinical tasks. Here, we present PathOrchestra, a versatile pathology foundation model trained via self-supervised learning on a dataset comprising 300K pathological slides from 20 tissue and organ types across multiple centers. The model was rigorously evaluated on 112 clinical tasks using a combination of 61 private and 51 public datasets. These tasks encompass digital slide preprocessing, pan-cancer classification, lesion identification, multi-cancer subtype classification, biomarker assessment, gene expression prediction, and the generation of structured reports. PathOrchestra demonstrated exceptional performance across 27,755 WSIs and 9,415,729 ROIs, achieving over 0.950 accuracy in 47 tasks, including pan-cancer classification across various organs, lymphoma subtype diagnosis, and bladder cancer screening. Notably, it is the first model to generate structured reports for high-incidence colorectal cancer and diagnostically complex lymphoma-areas that are infrequently addressed by foundational models but hold immense clinical potential. Overall, PathOrchestra exemplifies the feasibility and efficacy of a large-scale, self-supervised pathology foundation model, validated across a broad range of clinical-grade tasks. Its high accuracy and reduced reliance on extensive data annotation underline its potential for clinical integration, offering a pathway toward more efficient and high-quality medical services.

Xinzheng Wu, Junyi Chen, Jianfeng Wu et al.

Testing and evaluation is an important step before the large-scale application of the autonomous driving systems (ADSs). Based on the three level of scenario abstraction theory, a testing can be performed within a logical scenario, followed by an evaluation stage which is inputted with the testing results of each concrete scenario generated from the logical parameter space. During the above process, abundant testing information is produced which is beneficial for comprehensive and accurate evaluations. To make full use of testing information, this paper proposes an Integrated accelerated Testing and Evaluation Method (ITEM). Based on a Monte Carlo Tree Search (MCTS) paradigm and a dual surrogates testing framework proposed in our previous work, this paper applies the intermediate information (i.e., the tree structure, including the affiliation of each historical sampled point with the subspaces and the parent-child relationship between subspaces) generated during the testing stage into the evaluation stage to achieve accurate hazardous domain identification. Moreover, to better serve this purpose, the UCB calculation method is improved to allow the search algorithm to focus more on the hazardous domain boundaries. Further, a stopping condition is constructed based on the convergence of the search algorithm. Ablation and comparative experiments are then conducted to verify the effectiveness of the improvements and the superiority of the proposed method. The experimental results show that ITEM could well identify the hazardous domains in both low- and high-dimensional cases, regardless of the shape of the hazardous domains, indicating its generality and potential for the safety evaluation of ADSs.

Jianfeng Wu, Nannan Xu

Single image super-resolution is a well-known downstream task which aims to restore low-resolution images into high-resolution images. At present, models based on Transformers have shone brightly in the field of super-resolution due to their ability to capture long-term dependencies in information. However, current methods typically compute self-attention in nonoverlapping windows to save computational costs, and the standard self-attention computation only focuses on its results, thereby neglecting the useful information across channels and the rich spatial structural information generated in the intermediate process. Channel attention and spatial attention have, respectively, brought significant improvements to various downstream visual tasks in terms of extracting feature dependency and spatial structure relationships, but the synergistic relationship between channel and spatial attention has not been fully explored yet.To address these issues, we propose a novel model. Synergistic Alternating Aggregation Transformer (SAAT), which can better utilize the potential information of features. In SAAT, we introduce the Efficient Channel & Window Synergistic Attention Group (CWSAG) and the Spatial & Window Synergistic Attention Group (SWSAG). On the one hand, CWSAG combines efficient channel attention with shifted window attention, enhancing non-local feature fusion, and producing more visually appealing results. On the other hand, SWSAG leverages spatial attention to capture rich structured feature information, thereby enabling SAAT to more effectively extract structural features.Extensive experimental results and ablation studies demonstrate the effectiveness of SAAT in the field of super-resolution. SAAT achieves performance comparable to that of the state-of-the-art (SOTA) under the same quantity of parameters.

Jianfeng Wu, Wenhui Zhu, Yi Su et al.

Biomarker-assisted diagnosis and intervention in Alzheimer's disease (AD) may be the key to prevention breakthroughs. One of the hallmarks of AD is the accumulation of tau plaques in the human brain. However, current methods to detect tau pathology are either invasive (lumbar puncture) or quite costly and not widely available (Tau PET). In our previous work, structural MRI-based hippocampal multivariate morphometry statistics (MMS) showed superior performance as an effective neurodegenerative biomarker for preclinical AD and Patch Analysis-based Surface Correntropy-induced Sparse coding and max-pooling (PASCS-MP) has excellent ability to generate low-dimensional representations with strong statistical power for brain amyloid prediction. In this work, we apply this framework together with ridge regression models to predict Tau deposition in Braak12 and Braak34 brain regions separately. We evaluate our framework on 925 subjects from the Alzheimer's Disease Neuroimaging Initiative (ADNI). Each subject has one pair consisting of a PET image and MRI scan which were collected at about the same times. Experimental results suggest that the representations from our MMS and PASCS-MP have stronger predictive power and their predicted Braak12 and Braak34 are closer to the real values compared to the measures derived from other approaches such as hippocampal surface area and volume, and shape morphometry features based on spherical harmonics (SPHARM).

Jianfeng Wu, Sijie Mai, Haifeng Hu

Humans express their opinions and emotions through multiple modalities which mainly consist of textual, acoustic and visual modalities. Prior works on multimodal sentiment analysis mostly apply Recurrent Neural Network (RNN) to model aligned multimodal sequences. However, it is unpractical to align multimodal sequences due to different sample rates for different modalities. Moreover, RNN is prone to the issues of gradient vanishing or exploding and it has limited capacity of learning long-range dependency which is the major obstacle to model unaligned multimodal sequences. In this paper, we introduce Graph Capsule Aggregation (GraphCAGE) to model unaligned multimodal sequences with graph-based neural model and Capsule Network. By converting sequence data into graph, the previously mentioned problems of RNN are avoided. In addition, the aggregation capability of Capsule Network and the graph-based structure enable our model to be interpretable and better solve the problem of long-range dependency. Experimental results suggest that GraphCAGE achieves state-of-the-art performance on two benchmark datasets with representations refined by Capsule Network and interpretation provided.

Gang Wang, Qunxi Dong, Jianfeng Wu et al.

Cognitive decline due to Alzheimer's disease (AD) is closely associated with brain structure alterations captured by structural magnetic resonance imaging (sMRI). It supports the validity to develop sMRI-based univariate neurodegeneration biomarkers (UNB). However, existing UNB work either fails to model large group variances or does not capture AD dementia (ADD) induced changes. We propose a novel low-rank and sparse subspace decomposition method capable of stably quantifying the morphological changes induced by ADD. Specifically, we propose a numerically efficient rank minimization mechanism to extract group common structure and impose regularization constraints to encode the original 3D morphometry connectivity. Further, we generate regions-of-interest (ROI) with group difference study between common subspaces of $Aβ+$ AD and $Aβ-$ cognitively unimpaired (CU) groups. A univariate morphometry index (UMI) is constructed from these ROIs by summarizing individual morphological characteristics weighted by normalized difference between $Aβ+$ AD and $Aβ-$ CU groups. We use hippocampal surface radial distance feature to compute the UMIs and validate our work in the Alzheimer's Disease Neuroimaging Initiative (ADNI) cohort. With hippocampal UMIs, the estimated minimum sample sizes needed to detect a 25$\%$ reduction in the mean annual change with 80$\%$ power and two-tailed $P=0.05$ are 116, 279 and 387 for the longitudinal $Aβ+$ AD, $Aβ+$ mild cognitive impairment (MCI) and $Aβ+$ CU groups, respectively. Additionally, for MCI patients, UMIs well correlate with hazard ratio of conversion to AD ($4.3$, $95\%$ CI=$2.3-8.2$) within 18 months. Our experimental results outperform traditional hippocampal volume measures and suggest the application of UMI as a potential UNB.