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No existing work on visual question answering explicitly accounts for ambiguity regarding where the content described in the question is located in the image. To fill this gap, we introduce VQ-FocusAmbiguity, the first VQA dataset that visually grounds each region described in the question that is necessary to arrive at the answer. We then provide an analysis showing how our dataset for visually grounding `questions' is distinct from visually grounding `answers', and characterize the properties of the questions and segmentations provided in our dataset. Finally, we benchmark modern models for two novel tasks: recognizing whether a visual question has focus ambiguity and localizing all plausible focus regions within the image. Results show that the dataset is challenging for modern models. To facilitate future progress on these tasks, we publicly share the dataset with an evaluation server at https://focusambiguity.github.io/.

Vision language models can now generate long-form answers to questions about images - long-form visual question answers (LFVQA). We contribute VizWiz-LF, a dataset of long-form answers to visual questions posed by blind and low vision (BLV) users. VizWiz-LF contains 4.2k long-form answers to 600 visual questions, collected from human expert describers and six VQA models. We develop and annotate functional roles of sentences of LFVQA and demonstrate that long-form answers contain information beyond the question answer such as explanations and suggestions. We further conduct automatic and human evaluations with BLV and sighted people to evaluate long-form answers. BLV people perceive both human-written and generated long-form answers to be plausible, but generated answers often hallucinate incorrect visual details, especially for unanswerable visual questions (e.g., blurry or irrelevant images). To reduce hallucinations, we evaluate the ability of VQA models to abstain from answering unanswerable questions across multiple prompting strategies., Comment: COLM 2024

While there is much excitement about the potential of large multimodal models (LMM), a comprehensive evaluation is critical to establish their true capabilities and limitations. In support of this aim, we evaluate two state-of-the-art LMMs, GPT-4V and Gemini, on a new visual question answering dataset sourced from an authentic online question answering community. We conduct fine-grained analysis by generating seven types of metadata for nearly 2,000 visual questions, such as image type and the required image processing capabilities. Our zero-shot performance analysis highlights the types of questions that are most challenging for both models, including questions related to "puzzling" topic, with "Identification" user intention, with "Sheet Music" image type, or labeled as "hard" by GPT-4., Comment: 20 pages

Visual Question Answering (VQA) entails answering questions about images. We introduce the first VQA dataset in which all contents originate from an authentic use case. Sourced from online question answering community forums, we call it VQAonline. We characterize this dataset and how it relates to eight mainstream VQA datasets. Observing that answers in our dataset tend to be much longer (i.e., a mean of 173 words) and so incompatible with standard VQA evaluation metrics, we instead utilize popular metrics for longer text evaluation for evaluating six state-of-the-art VQA models on VQAonline and report where they struggle most. Finally, we analyze which evaluation metrics align best with human judgments. To facilitate future extensions, we publicly-share the dataset at: https://vqaonline.github.io/.

Visual question answering is a task of predicting the answer to a question about an image. Given that different people can provide different answers to a visual question, we aim to better understand why with answer groundings. We introduce the first dataset that visually grounds each unique answer to each visual question, which we call VQAAnswerTherapy. We then propose two novel problems of predicting whether a visual question has a single answer grounding and localizing all answer groundings. We benchmark modern algorithms for these novel problems to show where they succeed and struggle. The dataset and evaluation server can be found publicly at https://vizwiz.org/tasks-and-datasets/vqa-answer-therapy/., Comment: IEEE/CVF International Conference on Computer Vision

Visual question answering is the task of answering questions about images. We introduce the VizWiz-VQA-Grounding dataset, the first dataset that visually grounds answers to visual questions asked by people with visual impairments. We analyze our dataset and compare it with five VQA-Grounding datasets to demonstrate what makes it similar and different. We then evaluate the SOTA VQA and VQA-Grounding models and demonstrate that current SOTA algorithms often fail to identify the correct visual evidence where the answer is located. These models regularly struggle when the visual evidence occupies a small fraction of the image, for images that are higher quality, as well as for visual questions that require skills in text recognition. The dataset, evaluation server, and leaderboard all can be found at the following link: https://vizwiz.org/tasks-and-datasets/answer-grounding-for-vqa/., Comment: Computer Vision and Pattern Recognition

Building a highly accurate predictive model for classification and localization of abnormalities in chest X-rays usually requires a large number of manually annotated labels and pixel regions (bounding boxes) of abnormalities. However, it is expensive to acquire such annotations, especially the bounding boxes. Recently, contrastive learning has shown strong promise in leveraging unlabeled natural images to produce highly generalizable and discriminative features. However, extending its power to the medical image domain is under-explored and highly non-trivial, since medical images are much less amendable to data augmentations. In contrast, their prior knowledge, as well as radiomic features, is often crucial. To bridge this gap, we propose an end-to-end semi-supervised knowledge-augmented contrastive learning framework, that simultaneously performs disease classification and localization tasks. The key knob of our framework is a unique positive sampling approach tailored for the medical images, by seamlessly integrating radiomic features as a knowledge augmentation. Specifically, we first apply an image encoder to classify the chest X-rays and to generate the image features. We next leverage Grad-CAM to highlight the crucial (abnormal) regions for chest X-rays (even when unannotated), from which we extract radiomic features. The radiomic features are then passed through another dedicated encoder to act as the positive sample for the image features generated from the same chest X-ray. In this way, our framework constitutes a feedback loop for image and radiomic modality features to mutually reinforce each other. Their contrasting yields knowledge-augmented representations that are both robust and interpretable. Extensive experiments on the NIH Chest X-ray dataset demonstrate that our approach outperforms existing baselines in both classification and localization tasks., Comment: Accepted by WACV 2022

Chest X-ray becomes one of the most common medical diagnoses due to its noninvasiveness. The number of chest X-ray images has skyrocketed, but reading chest X-rays still have been manually performed by radiologists, which creates huge burnouts and delays. Traditionally, radiomics, as a subfield of radiology that can extract a large number of quantitative features from medical images, demonstrates its potential to facilitate medical imaging diagnosis before the deep learning era. With the rise of deep learning, the explainability of deep neural networks on chest X-ray diagnosis remains opaque. In this study, we proposed a novel framework that leverages radiomics features and contrastive learning to detect pneumonia in chest X-ray. Experiments on the RSNA Pneumonia Detection Challenge dataset show that our model achieves superior results to several state-of-the-art models (> 10% in F1-score) and increases the model's interpretability., Comment: Accepted for ISBI 2021

Chest X-ray becomes one of the most common medical diagnoses due to its noninvasiveness. The number of chest X-ray images has skyrocketed, but reading chest X-rays still have been manually performed by radiologists, which creates huge burnouts and delays. Traditionally, radiomics, as a subfield of radiology that can extract a large number of quantitative features from medical images, demonstrates its potential to facilitate medical imaging diagnosis before the deep learning era. In this paper, we develop an end-to-end framework, ChexRadiNet, that can utilize the radiomics features to improve the abnormality classification performance. Specifically, ChexRadiNet first applies a light-weight but efficient triplet-attention mechanism to classify the chest X-rays and highlight the abnormal regions. Then it uses the generated class activation map to extract radiomic features, which further guides our model to learn more robust image features. After a number of iterations and with the help of radiomic features, our framework can converge to more accurate image regions. We evaluate the ChexRadiNet framework using three public datasets: NIH ChestX-ray, CheXpert, and MIMIC-CXR. We find that ChexRadiNet outperforms the state-of-the-art on both disease detection (0.843 in AUC) and localization (0.679 in T(IoU) = 0.1). We will make the code publicly available at https://github.com/bionlplab/lung_disease_detection_amia2021, with the hope that this method can facilitate the development of automatic systems with a higher-level understanding of the radiological world., Comment: Accepted by AMIA 2021

Scientific novelty drives the efforts to invent new vaccines and solutions during the pandemic. First-time collaboration and international collaboration are two pivotal channels to expand teams' search activities for a broader scope of resources required to address the global challenge, which might facilitate the generation of novel ideas. Our analysis of 98,981 coronavirus papers suggests that scientific novelty measured by the BioBERT model that is pre-trained on 29 million PubMed articles, and first-time collaboration increased after the outbreak of COVID-19, and international collaboration witnessed a sudden decrease. During COVID-19, papers with more first-time collaboration were found to be more novel and international collaboration did not hamper novelty as it had done in the normal periods. The findings suggest the necessity of reaching out for distant resources and the importance of maintaining a collaborative scientific community beyond nationalism during a pandemic., Comment: 19 pages, 3 figures

The emergence of the novel COVID-19 pandemic has had a significant impact on global healthcare and the economy over the past few months. The virus's rapid widespread has led to a proliferation in biomedical research addressing the pandemic and its related topics. One of the essential Knowledge Discovery tools that could help the biomedical research community understand and eventually find a cure for COVID-19 are Knowledge Graphs. The CORD-19 dataset is a collection of publicly available full-text research articles that have been recently published on COVID-19 and coronavirus topics. Here, we use several Machine Learning, Deep Learning, and Knowledge Graph construction and mining techniques to formalize and extract insights from the PubMed dataset and the CORD-19 dataset to identify COVID-19 related experts and bio-entities. Besides, we suggest possible techniques to predict related diseases, drug candidates, gene, gene mutations, and related compounds as part of a systematic effort to apply Knowledge Discovery methods to help biomedical researchers tackle the pandemic., Comment: 8 pages; Accepted by ACM KDD 2020

PubMed is an essential resource for the medical domain, but useful concepts are either difficult to extract or are ambiguated, which has significantly hindered knowledge discovery. To address this issue, we constructed a PubMed knowledge graph (PKG) by extracting bio-entities from 29 million PubMed abstracts, disambiguating author names, integrating funding data through the National Institutes of Health (NIH) ExPORTER, collecting affiliation history and educational background of authors from ORCID, and identifying fine-grained affiliation data from MapAffil. Through the integration of the credible multi-source data, we could create connections among the bio-entities, authors, articles, affiliations, and funding. Data validation revealed that the BioBERT deep learning method of bio-entity extraction significantly outperformed the state-of-the-art models based on the F1 score (by 0.51%), with the author name disambiguation (AND) achieving a F1 score of 98.09%. PKG can trigger broader innovations, not only enabling us to measure scholarly impact, knowledge usage, and knowledge transfer, but also assisting us in profiling authors and organizations based on their connections with bio-entities. The PKG is freely available on Figshare (https://figshare.com/s/6327a55355fc2c99f3a2, simplified version that exclude PubMed raw data) and TACC website (http://er.tacc.utexas.edu/datasets/ped, full version)., Comment: 19 pages, 5 figures, 14 tables