Yijiang Chen

Fan Fan, Georgia Martinez, Thomas Desilvio et al.

Batch effects (BEs) refer to systematic technical differences in data collection unrelated to biological variations whose noise is shown to negatively impact machine learning (ML) model generalizability. Here we release CohortFinder, an open-source tool aimed at mitigating BEs via data-driven cohort partitioning. We demonstrate CohortFinder improves ML model performance in downstream medical image processing tasks. CohortFinder is freely available for download at cohortfinder.com.

Qian Da, Yijiang Chen, Min Ju et al.

Recent breakthroughs in artificial intelligence through foundation models and agents have accelerated the evolution of computational pathology. Demonstrated performance gains reported across academia in benchmarking datasets in predictive tasks such as diagnosis, prognosis, and treatment response have ignited substantial enthusiasm for clinical application. Despite this development momentum, real world adoption has lagged, as implementation faces economic, technical, and administrative challenges. Beyond existing discussions of technical architectures and comparative performance, this review considers how these emerging AI systems can be responsibly integrated into medical practice by connecting deployable clinical relevance with downstream analytical capabilities and their technical maturity, operational readiness, and economic and regulatory context. Drawing on perspectives from an international group, we provide a practical assessment of current capabilities and barriers to adoption in patient care settings.

Zhen Xing, Yijiang Chen, Zhixin Ling et al.

3D reconstruction of novel categories based on few-shot learning is appealing in real-world applications and attracts increasing research interests. Previous approaches mainly focus on how to design shape prior models for different categories. Their performance on unseen categories is not very competitive. In this paper, we present a Memory Prior Contrastive Network (MPCN) that can store shape prior knowledge in a few-shot learning based 3D reconstruction framework. With the shape memory, a multi-head attention module is proposed to capture different parts of a candidate shape prior and fuse these parts together to guide 3D reconstruction of novel categories. Besides, we introduce a 3D-aware contrastive learning method, which can not only complement the retrieval accuracy of memory network, but also better organize image features for downstream tasks. Compared with previous few-shot 3D reconstruction methods, MPCN can handle the inter-class variability without category annotations. Experimental results on a benchmark synthetic dataset and the Pascal3D+ real-world dataset show that our model outperforms the current state-of-the-art methods significantly.

Jinxi Xiang, Mingjie Li, Siyu Hou et al.

Accurate diagnosis and treatment of complex diseases require integrating histological, molecular, and clinical data, yet in practice these modalities are often incomplete owing to tissue scarcity, assay cost, and workflow constraints. Existing computational approaches attempt to impute missing modalities from available data but rely on task-specific models trained on narrow, single source-target pairs, limiting their generalizability. Here we introduce MuPD (Multimodal Pathology Diffusion), a generative foundation model that embeds hematoxylin and eosin (H&E)-stained histology, molecular RNA profiles, and clinical text into a shared latent space through a diffusion transformer with decoupled cross-modal attention. Pretrained on 100 million histology image patches, 1.6 million text-histology pairs, and 10.8 million RNA-histology pairs spanning 34 human organs, MuPD supports diverse cross-modal synthesis tasks with minimal or no task-specific fine-tuning. For text-conditioned and image-to-image generation, MuPD synthesizes histologically faithful tissue architectures, reducing Fréchet inception distance (FID) scores by 50% relative to domain-specific models and improving few-shot classification accuracy by up to 47% through synthetic data augmentation. For RNA-conditioned histology generation, MuPD reduces FID by 23% compared with the next-best method while preserving cell-type distributions across five cancer types. As a virtual stainer, MuPD translates H&E images to immunohistochemistry and multiplex immunofluorescence, improving average marker correlation by 37% over existing approaches. These results demonstrate that a single, unified generative model pretrained across heterogeneous pathology modalities can substantially outperform specialized alternatives, providing a scalable computational framework for multimodal histopathology.

Weijie Chen, Yongzhu Chang, Rongsheng Zhang et al.

Simile interpretation (SI) and simile generation (SG) are challenging tasks for NLP because models require adequate world knowledge to produce predictions. Previous works have employed many hand-crafted resources to bring knowledge-related into models, which is time-consuming and labor-intensive. In recent years, pre-trained language models (PLMs) based approaches have become the de-facto standard in NLP since they learn generic knowledge from a large corpus. The knowledge embedded in PLMs may be useful for SI and SG tasks. Nevertheless, there are few works to explore it. In this paper, we probe simile knowledge from PLMs to solve the SI and SG tasks in the unified framework of simile triple completion for the first time. The backbone of our framework is to construct masked sentences with manual patterns and then predict the candidate words in the masked position. In this framework, we adopt a secondary training process (Adjective-Noun mask Training) with the masked language model (MLM) loss to enhance the prediction diversity of candidate words in the masked position. Moreover, pattern ensemble (PE) and pattern search (PS) are applied to improve the quality of predicted words. Finally, automatic and human evaluations demonstrate the effectiveness of our framework in both SI and SG tasks.

Yijiang Chen, Xiangdong Zhou, Zhen Xing et al.

Self-supervised representation learning of Multivariate Time Series (MTS) is a challenging task and attracts increasing research interests in recent years. Many previous works focus on the pretext task of self-supervised learning and usually neglect the complex problem of MTS encoding, leading to unpromising results. In this paper, we tackle this challenge from two aspects: encoder and pretext task, and propose a unified channel-aware self-supervised learning framework CaSS. Specifically, we first design a new Transformer-based encoder Channel-aware Transformer (CaT) to capture the complex relationships between different time channels of MTS. Second, we combine two novel pretext tasks Next Trend Prediction (NTP) and Contextual Similarity (CS) for the self-supervised representation learning with our proposed encoder. Extensive experiments are conducted on several commonly used benchmark datasets. The experimental results show that our framework achieves new state-of-the-art comparing with previous self-supervised MTS representation learning methods (up to +7.70\% improvement on LSST dataset) and can be well applied to the downstream MTS classification.

Zhidan Liu, Zhen Xing, Xiangdong Zhou et al.

Image-based object pose estimation sounds amazing because in real applications the shape of object is oftentimes not available or not easy to take like photos. Although it is an advantage to some extent, un-explored shape information in 3D vision learning problem looks like "flaws in jade". In this paper, we deal with the problem in a reasonable new setting, namely 3D shape is exploited in the training process, and the testing is still purely image-based. We enhance the performance of image-based methods for category-agnostic object pose estimation by exploiting 3D knowledge learned by a multi-modal method. Specifically, we propose a novel contrastive knowledge distillation framework that effectively transfers 3D-augmented image representation from a multi-modal model to an image-based model. We integrate contrastive learning into the two-stage training procedure of knowledge distillation, which formulates an advanced solution to combine these two approaches for cross-modal tasks. We experimentally report state-of-the-art results compared with existing category-agnostic image-based methods by a large margin (up to +5% improvement on ObjectNet3D dataset), demonstrating the effectiveness of our method.

Jinxi Xiang, Siyu Hou, Yuchen Li et al.

Spatial transcriptomics (ST) enables gene expression mapping within anatomical context but remains costly and low-throughput. Hematoxylin and eosin (H\&E) staining offers rich morphology yet lacks molecular resolution. We present \textbf{\ours} (\textbf{S}patial \textbf{T}ranscriptomics and hist\textbf{O}logy \textbf{R}epresentation \textbf{M}odel), a foundation model trained on 1.2 million spatially resolved transcriptomic profiles with matched histology across 18 organs. Using a hierarchical architecture integrating morphological features, gene expression, and spatial context, STORM bridges imaging and omics through robust molecular--morphological representations. STORM enhances spatial domain discovery, producing biologically coherent tissue maps, and outperforms existing methods in predicting spatial gene expression from H\&E images across 11 tumor types. The model is platform-agnostic, performing consistently across Visium, Xenium, Visium HD, and CosMx. Applied to 23 independent cohorts comprising 7,245 patients, STORM significantly improves immunotherapy response prediction and prognostication over established biomarkers, providing a scalable framework for spatially informed discovery and clinical precision medicine.

Xiangde Luo, Xiyue Wang, Feyisope Eweje et al.

Histopathology is essential for disease diagnosis and treatment decision-making. Recent advances in artificial intelligence (AI) have enabled the development of pathology foundation models that learn rich visual representations from large-scale whole-slide images (WSIs). However, existing models are often trained on disparate datasets using varying strategies, leading to inconsistent performance and limited generalizability. Here, we introduce ELF (Ensemble Learning of Foundation models), a novel framework that integrates five state-of-the-art pathology foundation models to generate unified slide-level representations. Trained on 53,699 WSIs spanning 20 anatomical sites, ELF leverages ensemble learning to capture complementary information from diverse models while maintaining high data efficiency. Unlike traditional tile-level models, ELF's slide-level architecture is particularly advantageous in clinical contexts where data are limited, such as therapeutic response prediction. We evaluated ELF across a wide range of clinical applications, including disease classification, biomarker detection, and response prediction to major anticancer therapies, cytotoxic chemotherapy, targeted therapy, and immunotherapy, across multiple cancer types. ELF consistently outperformed all constituent foundation models and existing slide-level models, demonstrating superior accuracy and robustness. Our results highlight the power of ensemble learning for pathology foundation models and suggest ELF as a scalable and generalizable solution for advancing AI-assisted precision oncology.

Chengdong Liang, Yijiang Chen, Jiadi Yao et al.

Speaker verification based on ad-hoc microphone arrays has the potential of reducing the error significantly in adverse acoustic environments. However, existing approaches extract utterance-level speaker embeddings from each channel of an ad-hoc microphone array, which does not consider fully the spatial-temporal information across the devices. In this paper, we propose to aggregate the multichannel signals of the ad-hoc microphone array at the frame-level by exploring the cross-channel information deeply with two attention mechanisms. The first one is a self-attention method. It consists of a cross-frame self-attention layer and a cross-channel self-attention layer successively, both working at the frame level. The second one learns the cross-frame and cross-channel information via two graph attention layers. Experimental results demonstrate that the proposed methods reach the state-of-the-art performance. Moreover, the graph-attention method is better than the self-attention method in most cases.