Qifeng Zhou

Qifeng Zhou, Lei Yu, Yuzhi Guo et al.

The integration of single-cell proteomic data is often hindered by the fragmented nature of targeted antibody panels. To address this limitation, we introduce scpFormer, a transformer-based foundation model designed for single-cell proteomics. Pre-trained on over 390 million cells, scpFormer replaces standard index-based tokenization with a continuous, sequence-anchored approach. By combining Evolutionary Scale Modeling (ESM) with value-aware expression embeddings, it dynamically maps variable panels into a shared semantic space without artificial discretization. We demonstrate that scpFormer generates global cell representations that perform competitively in large-scale batch integration and unsupervised clustering. Moreover, its open-vocabulary architecture facilitates in silico panel expansion, assisting in the reconstruction of biological manifolds in sparse clinical datasets. Finally, this learned protein co-expression logic is transferable to bulk-omics tasks, supporting applications like cancer drug response prediction. scpFormer provides a versatile, panel-agnostic framework to facilitate scalable biomarker discovery and precision oncology.

Yaohui Li, Qifeng Zhou, Haoxing Chen et al.

Contrastive Language-Image Pre-training (CLIP) has shown powerful zero-shot learning performance. Few-shot learning aims to further enhance the transfer capability of CLIP by giving few images in each class, aka 'few shots'. Most existing methods either implicitly learn from the few shots by incorporating learnable prompts or adapters, or explicitly embed them in a cache model for inference. However, the narrow distribution of few shots often contains incomplete class information, leading to biased visual knowledge with high risk of misclassification. To tackle this problem, recent methods propose to supplement visual knowledge by generative models or extra databases, which can be costly and time-consuming. In this paper, we propose an Iterative Visual Knowledge CompLetion (KCL) method to complement visual knowledge by properly taking advantages of unlabeled samples without access to any auxiliary or synthetic data. Specifically, KCL first measures the similarities between unlabeled samples and each category. Then, the samples with top confidence to each category is selected and collected by a designed confidence criterion. Finally, the collected samples are treated as labeled ones and added to few shots to jointly re-estimate the remaining unlabeled ones. The above procedures will be repeated for a certain number of iterations with more and more samples being collected until convergence, ensuring a progressive and robust knowledge completion process. Extensive experiments on 11 benchmark datasets demonstrate the effectiveness and efficiency of KCL as a plug-and-play module under both few-shot and zero-shot learning settings. Code is available at https://github.com/Mark-Sky/KCL.

Haiqing Li, Yuzhi Guo, Feng Jiang et al.

Early-stage scoliosis is often difficult to detect, particularly in adolescents, where delayed diagnosis can lead to serious health issues. Traditional X-ray-based methods carry radiation risks and rely heavily on clinical expertise, limiting their use in large-scale screenings. To overcome these challenges, we propose a Text-Guided Multi-Instance Learning Network (TG-MILNet) for non-invasive scoliosis detection using gait videos. To handle temporal misalignment in gait sequences, we employ Dynamic Time Warping (DTW) clustering to segment videos into key gait phases. To focus on the most relevant diagnostic features, we introduce an Inter-Bag Temporal Attention (IBTA) mechanism that highlights critical gait phases. Recognizing the difficulty in identifying borderline cases, we design a Boundary-Aware Model (BAM) to improve sensitivity to subtle spinal deviations. Additionally, we incorporate textual guidance from domain experts and large language models (LLM) to enhance feature representation and improve model interpretability. Experiments on the large-scale Scoliosis1K gait dataset show that TG-MILNet achieves state-of-the-art performance, particularly excelling in handling class imbalance and accurately detecting challenging borderline cases. The code is available at https://github.com/lhqqq/TG-MILNet

Qifeng Zhou, Wenliang Zhong, Yuzhi Guo et al.

In the field of computational histopathology, both whole slide images (WSIs) and diagnostic captions provide valuable insights for making diagnostic decisions. However, aligning WSIs with diagnostic captions presents a significant challenge. This difficulty arises from two main factors: 1) Gigapixel WSIs are unsuitable for direct input into deep learning models, and the redundancy and correlation among the patches demand more attention; and 2) Authentic WSI diagnostic captions are extremely limited, making it difficult to train an effective model. To overcome these obstacles, we present PathM3, a multimodal, multi-task, multiple instance learning (MIL) framework for WSI classification and captioning. PathM3 adapts a query-based transformer to effectively align WSIs with diagnostic captions. Given that histopathology visual patterns are redundantly distributed across WSIs, we aggregate each patch feature with MIL method that considers the correlations among instances. Furthermore, our PathM3 overcomes data scarcity in WSI-level captions by leveraging limited WSI diagnostic caption data in the manner of multi-task joint learning. Extensive experiments with improved classification accuracy and caption generation demonstrate the effectiveness of our method on both WSI classification and captioning task.

Haiqing Li, Yuzhi Guo, Feng Jiang et al.

Scoliosis is a spinal curvature disorder that is difficult to detect early and can compress the chest cavity, impacting respiratory function and cardiac health. Especially for adolescents, delayed detection and treatment result in worsening compression. Traditional scoliosis detection methods heavily rely on clinical expertise, and X-ray imaging poses radiation risks, limiting large-scale early screening. We propose an Attention-Guided Deep Multi-Instance Learning method (Gait-MIL) to effectively capture discriminative features from gait patterns, which is inspired by ScoNet-MT's pioneering use of gait patterns for scoliosis detection. We evaluate our method on the first large-scale dataset based on gait patterns for scoliosis classification. The results demonstrate that our study improves the performance of using gait as a biomarker for scoliosis detection, significantly enhances detection accuracy for the particularly challenging Neutral cases, where subtle indicators are often overlooked. Our Gait-MIL also performs robustly in imbalanced scenarios, making it a promising tool for large-scale scoliosis screening.

Qifeng Zhou, Thao M. Dang, Wenliang Zhong et al.

Pathology plays a critical role in diagnosing a wide range of diseases, yet existing approaches often rely heavily on task-specific models trained on extensive, well-labeled datasets. These methods face sustainability challenges due to the diversity of pathologies and the labor-intensive nature of data collection. To address these limitations, we highlight the need for universal multimodal embeddings that can support multiple downstream tasks. Previous approaches involve fine-tuning CLIP-based models, which handle images and texts separately, limiting their ability to capture complex multimodal relationships. Additionally, these models are evaluated across diverse datasets without a unified benchmark. In this paper, we explore the possibility of applying Multimodal Large Language Models (MLLMs) to generate pathology universal embeddings to address these challenges. Our contributions can be summarized in the following aspects: 1) We propose MLLM4PUE, a novel framework that leverages MLLMs to generate embeddings for various pathology downstream tasks. 2) We further introduce the Pathology Multimodal Embedding Benchmark (PMEB), a comprehensive benchmark designed to assess the quality of pathology multimodal embeddings, which comprises 16 original tasks drawn from 15 datasets. 3) Extensive experimental results demonstrate the superiority of MLLM4PUE, illustrating MLLM-based models can effectively support a wide range of downstream tasks and unify the research direction for foundation models in pathology.

Wei Xiao, Huiying Wang, Qifeng Zhou

Sequential recommendation is a key area in the field of recommendation systems aiming to model user interest based on historical interaction sequences with irregular intervals. While previous recurrent neural network-based and attention-based approaches have achieved significant results, they have limitations in capturing system continuity due to the discrete characteristics. In the context of continuous-time modeling, state space model (SSM) offers a potential solution, as it can effectively capture the dynamic evolution of user interest over time. However, existing SSM-based approaches ignore the impact of irregular time intervals within historical user interactions, making it difficult to model complexed user-item transitions in sequences. To address this issue, we propose a hybrid SSM-based model called SS4Rec for continuous-time sequential recommendation. SS4Rec integrates a time-aware SSM to handle irregular time intervals and a relation-aware SSM to model contextual dependencies, enabling it to infer user interest from both temporal and sequential perspectives. In the training process, the time-aware SSM and the relation-aware SSM are discretized by variable stepsizes according to user interaction time intervals and input data, respectively. This helps capture the continuous dependency from irregular time intervals and provides time-specific personalized recommendations. Experimental studies on five benchmark datasets demonstrate the superiority and effectiveness of SS4Rec.