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.
Generative AI systems such as ChatGPT and Claude are built upon language models that are typically evaluated for accuracy on curated benchmark datasets. Such evaluation paradigms measure predictive and reasoning capabilities of language models but do not assess if they can provide information that is useful to people. In this paper, we take some initial steps in developing an evaluation paradigm that centers human understanding and decision-making. We study the utility of generative AI systems in supporting people in a concrete task - making sense of clinical reports and imagery in order to make a clinical decision. We conducted a formative need-finding study in which participants discussed chest computed tomography (CT) scans and associated radiology reports of a fictitious close relative with a cardiothoracic radiologist. Using thematic analysis of the conversation between participants and medical experts, we identified commonly occurring themes across interactions, including clarifying medical terminology, locating the problems mentioned in the report in the scanned image, understanding disease prognosis, discussing the next diagnostic steps, and comparing treatment options. Based on these themes, we evaluated two state-of-the-art generative AI systems against the radiologist's responses. Our results reveal variability in the quality of responses generated by the models across various themes. We highlight the importance of patient-facing generative AI systems to accommodate a diverse range of conversational themes, catering to the real-world informational needs of patients.
Multi-modal tasks involving vision and language in deep learning continue to rise in popularity and are leading to the development of newer models that can generalize beyond the extent of their training data. The current models lack temporal generalization which enables models to adapt to changes in future data. This paper discusses a viable approach to creating an advanced Visual Question Answering (VQA) model which can produce successful results on temporal generalization. We propose a new data set, GenVQA, utilizing images and captions from the VQAv2 and MS-COCO dataset to generate new images through stable diffusion. This augmented dataset is then used to test a combination of seven baseline and cutting edge VQA models. Performance evaluation focuses on questions mirroring the original VQAv2 dataset, with the answers having been adjusted to the new images. This paper's purpose is to investigate the robustness of several successful VQA models to assess their performance on future data distributions. Model architectures are analyzed to identify common stylistic choices that improve generalization under temporal distribution shifts. This research highlights the importance of creating a large-scale future shifted dataset. This data can enhance the robustness of VQA models, allowing their future peers to have improved ability to adapt to temporal distribution shifts.
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.
Building models that can be rapidly adapted to novel tasks using only a handful of annotated examples is an open challenge for multimodal machine learning research. We introduce Flamingo, a family of Visual Language Models (VLM) with this ability. We propose key architectural innovations to: (i) bridge powerful pretrained vision-only and language-only models, (ii) handle sequences of arbitrarily interleaved visual and textual data, and (iii) seamlessly ingest images or videos as inputs. Thanks to their flexibility, Flamingo models can be trained on large-scale multimodal web corpora containing arbitrarily interleaved text and images, which is key to endow them with in-context few-shot learning capabilities. We perform a thorough evaluation of our models, exploring and measuring their ability to rapidly adapt to a variety of image and video tasks. These include open-ended tasks such as visual question-answering, where the model is prompted with a question which it has to answer; captioning tasks, which evaluate the ability to describe a scene or an event; and close-ended tasks such as multiple-choice visual question-answering. For tasks lying anywhere on this spectrum, a single Flamingo model can achieve a new state of the art with few-shot learning, simply by prompting the model with task-specific examples. On numerous benchmarks, Flamingo outperforms models fine-tuned on thousands of times more task-specific data.