Wenliang Zhong

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.

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.

Wenliang Zhong, Weizhi An, Feng Jiang et al.

Composed Image Retrieval (CIR) involves retrieving a target image based on a composed query of an image paired with text that specifies modifications or changes to the visual reference. CIR is inherently an instruction-following task, as the model needs to interpret and apply modifications to the image. In practice, due to the scarcity of annotated data in downstream tasks, Zero-Shot CIR (ZS-CIR) is desirable. While existing ZS-CIR models based on CLIP have shown promising results, their capability in interpreting and following modification instructions remains limited. Some research attempts to address this by incorporating Large Language Models (LLMs). However, these approaches still face challenges in effectively integrating multimodal information and instruction understanding. To tackle above challenges, we propose a novel embedding method utilizing an instruction-tuned Multimodal LLM (MLLM) to generate composed representation, which significantly enhance the instruction following capability for a comprehensive integration between images and instructions. Nevertheless, directly applying MLLMs introduces a new challenge since MLLMs are primarily designed for text generation rather than embedding extraction as required in CIR. To address this, we introduce a two-stage training strategy to efficiently learn a joint multimodal embedding space and further refining the ability to follow modification instructions by tuning the model in a triplet dataset similar to the CIR format. Extensive experiments on four public datasets: FashionIQ, CIRR, GeneCIS, and CIRCO demonstrates the superior performance of our model, outperforming state-of-the-art baselines by a significant margin. Codes are available at the GitHub repository.

Wenyi Wu, Qi Li, Wenliang Zhong et al.

Vision-language models have been widely explored across a wide range of tasks and achieve satisfactory performance. However, it's under-explored how to consolidate entity understanding through a varying number of images and to align it with the pre-trained language models for generative tasks. In this paper, we propose MIVC, a general multiple instance visual component to bridge the gap between various image inputs with off-the-shelf vision-language models by aggregating visual representations in a permutation-invariant fashion through a neural network. We show that MIVC could be plugged into the visual-language models to improve the model performance consistently on visual question answering, classification and captioning tasks on a public available e-commerce dataset with multiple images per product. Furthermore, we show that the component provides insight into the contribution of each image to the downstream tasks.

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.

Wenliang Zhong, Wenyi Wu, Qi Li et al.

Multimodal Large Language Models (MLLMs) have achieved SOTA performance in various visual language tasks by fusing the visual representations with LLMs leveraging some visual adapters. In this paper, we first establish that adapters using query-based Transformers such as Q-former is a simplified Multi-instance Learning method without considering instance heterogeneity/correlation. We then propose a general component termed Multi-instance Visual Prompt Generator (MIVPG) to incorporate enriched visual representations into LLMs by taking advantage of instance correlation between images or patches for the same sample. Quantatitive evaluation on three public vision-language (VL) datasets from different scenarios shows that the proposed MIVPG improves Q-former in main VL tasks.

Yucheng Shi, Hehuan Ma, Wenliang Zhong et al.

ChatGPT, as a recently launched large language model (LLM), has shown superior performance in various natural language processing (NLP) tasks. However, two major limitations hinder its potential applications: (1) the inflexibility of finetuning on downstream tasks and (2) the lack of interpretability in the decision-making process. To tackle these limitations, we propose a novel framework that leverages the power of ChatGPT for specific tasks, such as text classification, while improving its interpretability. The proposed framework conducts a knowledge graph extraction task to extract refined and structural knowledge from the raw data using ChatGPT. The rich knowledge is then converted into a graph, which is further used to train an interpretable linear classifier to make predictions. To evaluate the effectiveness of our proposed method, we conduct experiments on four datasets. The result shows that our method can significantly improve the performance compared to directly utilizing ChatGPT for text classification tasks. And our method provides a more transparent decision-making process compared with previous text classification methods.