Multimodal learning combining pathology images and genomic sequences enhances cancer survival analysis but faces clinical implementation barriers due to limited access to genomic sequencing in under-resourced regions. To enable survival prediction using only whole-slide images (WSI), we propose the Visual-Genomic Answering-Guided Transformer (VGAT), a framework integrating Visual Question Answering (VQA) techniques for genomic modality reconstruction. By adapting VQA's text feature extraction approach, we derive stable genomic representations that circumvent dimensionality challenges in raw genomic data. Simultaneously, a cluster-based visual prompt module selectively enhances discriminative WSI patches, addressing noise from unfiltered image regions. Evaluated across five TCGA datasets, VGAT outperforms existing WSI-only methods, demonstrating the viability of genomic-informed inference without sequencing. This approach bridges multimodal research and clinical feasibility in resource-constrained settings. The code link is https://github.com/CZZZZZZZZZZZZZZZZZ/VGAT.
Throughout rapid development of multimodal large language models, a crucial ingredient is a fair and accurate evaluation of their multimodal comprehension abilities. Although Visual Question Answering (VQA) could serve as a developed test field, limitations of VQA evaluation, like the inflexible pattern of Exact Match, have hindered MLLMs from demonstrating their real capability and discourage rich responses. Therefore, this paper proposes the use of semantics-based evaluators for assessing unconstrained open-ended responses on VQA datasets. As characteristics of VQA have made such evaluation significantly different than the traditional Semantic Textual Similarity (STS) task, to systematically analyze the behaviour and compare the performance of various evaluators including LLM-based ones, we proposes three key properties, i.e., Alignment, Consistency and Generalization, and a corresponding dataset Assessing VQA Evaluators (AVE) to facilitate analysis. In addition, this paper proposes a Semantically Flexible VQA Evaluator (SFVE) with meticulous design based on the unique features of VQA evaluation. Experimental results verify the feasibility of model-based VQA evaluation and effectiveness of the proposed evaluator that surpasses existing semantic evaluators by a large margin. The proposed training scheme generalizes to both the BERT-like encoders and decoder-only LLM.
Whole slide imaging is routinely adopted for carcinoma diagnosis and prognosis. Abundant experience is required for pathologists to achieve accurate and reliable diagnostic results of whole slide images (WSI). The huge size and heterogeneous features of WSIs make the workflow of pathological reading extremely time-consuming. In this paper, we propose a novel framework (WSI-VQA) to interpret WSIs by generative visual question answering. WSI-VQA shows universality by reframing various kinds of slide-level tasks in a question-answering pattern, in which pathologists can achieve immunohistochemical grading, survival prediction, and tumor subtyping following human-machine interaction. Furthermore, we establish a WSI-VQA dataset which contains 8672 slide-level question-answering pairs with 977 WSIs. Besides the ability to deal with different slide-level tasks, our generative model which is named Wsi2Text Transformer (W2T) outperforms existing discriminative models in medical correctness, which reveals the potential of our model to be applied in the clinical scenario. Additionally, we also visualize the co-attention mapping between word embeddings and WSIs as an intuitive explanation for diagnostic results. The dataset and related code are available at https://github.com/cpystan/WSI-VQA.
Recent years have witnessed impressive results of pre-trained vision-language models on knowledge-intensive tasks such as visual question answering (VQA). Despite the recent advances in VQA, existing methods mainly adopt a discriminative formulation that predicts answers within a pre-defined label set, leading to easy overfitting on low-resource domains with limited labeled data (e.g., medicine) and poor generalization under domain shift to another dataset. To tackle this limitation, we propose a novel generative model enhanced by multimodal prompt retrieval (MPR) that integrates retrieved prompts and multimodal features to generate answers in free text. Our generative model enables rapid zero-shot dataset adaptation to unseen data distributions and open-set answer labels across datasets. Our experiments on medical VQA tasks show that MPR outperforms its non-retrieval counterpart by up to 30% accuracy points in a few-shot domain adaptation setting.
Medical Visual Question Answering (MedVQA) presents a significant opportunity to enhance diagnostic accuracy and healthcare delivery by leveraging artificial intelligence to interpret and answer questions based on medical images. In this study, we reframe the problem of MedVQA as a generation task that naturally follows the human-machine interaction and propose a generative-based model for medical visual understanding by aligning visual information from a pre-trained vision encoder with a large language model. We establish a scalable pipeline to construct a large-scale medical visual question-answering dataset, named PMC-VQA, which contains 227k VQA pairs of 149k images that cover various modalities or diseases. We train the proposed model on PMC-VQA and then fine-tune it on multiple public benchmarks, e.g., VQA-RAD, SLAKE, and Image-Clef-2019, significantly outperforming existing MedVQA models in generating relevant, accurate free-form answers. In addition, we propose a test set that has undergone manual verification, which is significantly more challenging, serving to better monitor the development of generative MedVQA methods. To facilitate comprehensive evaluation and comparison, we have maintained a leaderboard at https://paperswithcode.com/paper/pmc-vqa-visual-instruction-tuning-for-medical, offering a centralized resource for tracking progress and benchmarking state-of-the-art approaches. The PMC-VQA dataset emerges as a vital resource for the field of research, and the MedVInT presents a significant breakthrough in the area of MedVQA.
The cost of vision-and-language pre-training has become increasingly prohibitive due to end-to-end training of large-scale models. This paper proposes BLIP-2, a generic and efficient pre-training strategy that bootstraps vision-language pre-training from off-the-shelf frozen pre-trained image encoders and frozen large language models. BLIP-2 bridges the modality gap with a lightweight Querying Transformer, which is pre-trained in two stages. The first stage bootstraps vision-language representation learning from a frozen image encoder. The second stage bootstraps vision-to-language generative learning from a frozen language model. BLIP-2 achieves state-of-the-art performance on various vision-language tasks, despite having significantly fewer trainable parameters than existing methods. For example, our model outperforms Flamingo80B by 8.7% on zero-shot VQAv2 with 54x fewer trainable parameters. We also demonstrate the model's emerging capabilities of zero-shot image-to-text generation that can follow natural language instructions.