Daily Papers

The COVID-19 pandemic caused great losses worldwide, efforts are taken place to prevent but many countries have failed. In Vietnam, the traceability, localization, and quarantine of people who contact with patients contribute to effective disease prevention. However, this is done by hand, and take a lot of work. In this research, we describe a named-entity recognition (NER) study that assists in the prevention of COVID-19 pandemic in Vietnam. We also present our manually annotated COVID-19 dataset with nested named entity recognition task for Vietnamese which be defined new entity types using for our system.

This technical report delves into the application of GPT-4 Vision (GPT-4V) in the nuanced realm of COVID-19 image classification, leveraging the transformative potential of in-context learning to enhance diagnostic processes.

The COVID-19 pandemic has spread globally for several months. Because its transmissibility and high pathogenicity seriously threaten people's lives, it is crucial to accurately and quickly detect COVID-19 infection. Many recent studies have shown that deep learning (DL) based solutions can help detect COVID-19 based on chest CT scans. However, most existing work focuses on 2D datasets, which may result in low quality models as the real CT scans are 3D images. Besides, the reported results span a broad spectrum on different datasets with a relatively unfair comparison. In this paper, we first use three state-of-the-art 3D models (ResNet3D101, DenseNet3D121, and MC3\_18) to establish the baseline performance on the three publicly available chest CT scan datasets. Then we propose a differentiable neural architecture search (DNAS) framework to automatically search for the 3D DL models for 3D chest CT scans classification with the Gumbel Softmax technique to improve the searching efficiency. We further exploit the Class Activation Mapping (CAM) technique on our models to provide the interpretability of the results. The experimental results show that our automatically searched models (CovidNet3D) outperform the baseline human-designed models on the three datasets with tens of times smaller model size and higher accuracy. Furthermore, the results also verify that CAM can be well applied in CovidNet3D for COVID-19 datasets to provide interpretability for medical diagnosis.

There has been much interest in accurate cryptocurrency price forecast models by investors and researchers. Deep Learning models are prominent machine learning techniques that have transformed various fields and have shown potential for finance and economics. Although various deep learning models have been explored for cryptocurrency price forecasting, it is not clear which models are suitable due to high market volatility. In this study, we review the literature about deep learning for cryptocurrency price forecasting and evaluate novel deep learning models for cryptocurrency stock price prediction. Our deep learning models include variants of long short-term memory (LSTM) recurrent neural networks, variants of convolutional neural networks (CNNs), and the Transformer model. We evaluate univariate and multivariate approaches for multi-step ahead predicting of cryptocurrencies close-price. We also carry out volatility analysis on the four cryptocurrencies which reveals significant fluctuations in their prices throughout the COVID-19 pandemic. Additionally, we investigate the prediction accuracy of two scenarios identified by different training sets for the models. First, we use the pre-COVID-19 datasets to model cryptocurrency close-price forecasting during the early period of COVID-19. Secondly, we utilise data from the COVID-19 period to predict prices for 2023 to 2024. Our results show that the convolutional LSTM with a multivariate approach provides the best prediction accuracy in two major experimental settings. Our results also indicate that the multivariate deep learning models exhibit better performance in forecasting four different cryptocurrencies when compared to the univariate models.

In this paper, we present ArCOV-19, an Arabic COVID-19 Twitter dataset that spans one year, covering the period from 27th of January 2020 till 31st of January 2021. ArCOV-19 is the first publicly-available Arabic Twitter dataset covering COVID-19 pandemic that includes about 2.7M tweets alongside the propagation networks of the most-popular subset of them (i.e., most-retweeted and -liked). The propagation networks include both retweets and conversational threads (i.e., threads of replies). ArCOV-19 is designed to enable research under several domains including natural language processing, information retrieval, and social computing. Preliminary analysis shows that ArCOV-19 captures rising discussions associated with the first reported cases of the disease as they appeared in the Arab world. In addition to the source tweets and propagation networks, we also release the search queries and language-independent crawler used to collect the tweets to encourage the curation of similar datasets.

The global ramifications of the COVID-19 pandemic remain significant, exerting persistent pressure on nations even three years after its initial outbreak. Deep learning models have shown promise in improving COVID-19 diagnostics but require diverse and larger-scale datasets to improve performance. In this paper, we introduce COVIDx CXR-4, an expanded multi-institutional open-source benchmark dataset for chest X-ray image-based computer-aided COVID-19 diagnostics. COVIDx CXR-4 expands significantly on the previous COVIDx CXR-3 dataset by increasing the total patient cohort size by greater than 2.66 times, resulting in 84,818 images from 45,342 patients across multiple institutions. We provide extensive analysis on the diversity of the patient demographic, imaging metadata, and disease distributions to highlight potential dataset biases. To the best of the authors' knowledge, COVIDx CXR-4 is the largest and most diverse open-source COVID-19 CXR dataset and is made publicly available as part of an open initiative to advance research to aid clinicians against the COVID-19 disease.

Under the pandemic of COVID-19, people experiencing COVID19-related symptoms or exposed to risk factors have a pressing need to consult doctors. Due to hospital closure, a lot of consulting services have been moved online. Because of the shortage of medical professionals, many people cannot receive online consultations timely. To address this problem, we aim to develop a medical dialogue system that can provide COVID19-related consultations. We collected two dialogue datasets -- CovidDialog -- (in English and Chinese respectively) containing conversations between doctors and patients about COVID-19. On these two datasets, we train several dialogue generation models based on Transformer, GPT, and BERT-GPT. Since the two COVID-19 dialogue datasets are small in size, which bear high risk of overfitting, we leverage transfer learning to mitigate data deficiency. Specifically, we take the pretrained models of Transformer, GPT, and BERT-GPT on dialog datasets and other large-scale texts, then finetune them on our CovidDialog tasks. We perform both automatic and human evaluation of responses generated by these models. The results show that the generated responses are promising in being doctor-like, relevant to the conversation history, and clinically informative. The data and code are available at https://github.com/UCSD-AI4H/COVID-Dialogue.

The COVID-19 pandemic has posed a heavy burden to the healthcare system worldwide and caused huge social disruption and economic loss. Many deep learning models have been proposed to conduct clinical predictive tasks such as mortality prediction for COVID-19 patients in intensive care units using Electronic Health Record (EHR) data. Despite their initial success in certain clinical applications, there is currently a lack of benchmarking results to achieve a fair comparison so that we can select the optimal model for clinical use. Furthermore, there is a discrepancy between the formulation of traditional prediction tasks and real-world clinical practice in intensive care. To fill these gaps, we propose two clinical prediction tasks, Outcome-specific length-of-stay prediction and Early mortality prediction for COVID-19 patients in intensive care units. The two tasks are adapted from the naive length-of-stay and mortality prediction tasks to accommodate the clinical practice for COVID-19 patients. We propose fair, detailed, open-source data-preprocessing pipelines and evaluate 17 state-of-the-art predictive models on two tasks, including 5 machine learning models, 6 basic deep learning models and 6 deep learning predictive models specifically designed for EHR data. We provide benchmarking results using data from two real-world COVID-19 EHR datasets. One dataset is publicly available without needing any inquiry and another dataset can be accessed on request. We provide fair, reproducible benchmarking results for two tasks. We deploy all experiment results and models on an online platform. We also allow clinicians and researchers to upload their data to the platform and get quick prediction results using our trained models. We hope our efforts can further facilitate deep learning and machine learning research for COVID-19 predictive modeling.

As the COVID-19 virus quickly spreads around the world, unfortunately, misinformation related to COVID-19 also gets created and spreads like wild fire. Such misinformation has caused confusion among people, disruptions in society, and even deadly consequences in health problems. To be able to understand, detect, and mitigate such COVID-19 misinformation, therefore, has not only deep intellectual values but also huge societal impacts. To help researchers combat COVID-19 health misinformation, therefore, we present CoAID (Covid-19 heAlthcare mIsinformation Dataset), with diverse COVID-19 healthcare misinformation, including fake news on websites and social platforms, along with users' social engagement about such news. CoAID includes 4,251 news, 296,000 related user engagements, 926 social platform posts about COVID-19, and ground truth labels. The dataset is available at: https://github.com/cuilimeng/CoAID.

The COVID-19 Open Research Dataset (CORD-19) is a growing resource of scientific papers on COVID-19 and related historical coronavirus research. CORD-19 is designed to facilitate the development of text mining and information retrieval systems over its rich collection of metadata and structured full text papers. Since its release, CORD-19 has been downloaded over 200K times and has served as the basis of many COVID-19 text mining and discovery systems. In this article, we describe the mechanics of dataset construction, highlighting challenges and key design decisions, provide an overview of how CORD-19 has been used, and describe several shared tasks built around the dataset. We hope this resource will continue to bring together the computing community, biomedical experts, and policy makers in the search for effective treatments and management policies for COVID-19.

Along with COVID-19 pandemic we are also fighting an `infodemic'. Fake news and rumors are rampant on social media. Believing in rumors can cause significant harm. This is further exacerbated at the time of a pandemic. To tackle this, we curate and release a manually annotated dataset of 10,700 social media posts and articles of real and fake news on COVID-19. We benchmark the annotated dataset with four machine learning baselines - Decision Tree, Logistic Regression, Gradient Boost, and Support Vector Machine (SVM). We obtain the best performance of 93.46% F1-score with SVM. The data and code is available at: https://github.com/parthpatwa/covid19-fake-news-dectection

We present CovidQA, the beginnings of a question answering dataset specifically designed for COVID-19, built by hand from knowledge gathered from Kaggle's COVID-19 Open Research Dataset Challenge. To our knowledge, this is the first publicly available resource of its type, and intended as a stopgap measure for guiding research until more substantial evaluation resources become available. While this dataset, comprising 124 question-article pairs as of the present version 0.1 release, does not have sufficient examples for supervised machine learning, we believe that it can be helpful for evaluating the zero-shot or transfer capabilities of existing models on topics specifically related to COVID-19. This paper describes our methodology for constructing the dataset and presents the effectiveness of a number of baselines, including term-based techniques and various transformer-based models. The dataset is available at http://covidqa.ai/

The COVID-19 pandemic has threatened global health. Many studies have applied deep convolutional neural networks (CNN) to recognize COVID-19 based on chest 3D computed tomography (CT). Recent works show that no model generalizes well across CT datasets from different countries, and manually designing models for specific datasets requires expertise; thus, neural architecture search (NAS) that aims to search models automatically has become an attractive solution. To reduce the search cost on large 3D CT datasets, most NAS-based works use the weight-sharing (WS) strategy to make all models share weights within a supernet; however, WS inevitably incurs search instability, leading to inaccurate model estimation. In this work, we propose an efficient Evolutionary Multi-objective ARchitecture Search (EMARS) framework. We propose a new objective, namely potential, which can help exploit promising models to indirectly reduce the number of models involved in weights training, thus alleviating search instability. We demonstrate that under objectives of accuracy and potential, EMARS can balance exploitation and exploration, i.e., reducing search time and finding better models. Our searched models are small and perform better than prior works on three public COVID-19 3D CT datasets.

This paper introduces HeBERT and HebEMO. HeBERT is a Transformer-based model for modern Hebrew text, which relies on a BERT (Bidirectional Encoder Representations for Transformers) architecture. BERT has been shown to outperform alternative architectures in sentiment analysis, and is suggested to be particularly appropriate for MRLs. Analyzing multiple BERT specifications, we find that while model complexity correlates with high performance on language tasks that aim to understand terms in a sentence, a more-parsimonious model better captures the sentiment of entire sentence. Either way, out BERT-based language model outperforms all existing Hebrew alternatives on all common language tasks. HebEMO is a tool that uses HeBERT to detect polarity and extract emotions from Hebrew UGC. HebEMO is trained on a unique Covid-19-related UGC dataset that we collected and annotated for this study. Data collection and annotation followed an active learning procedure that aimed to maximize predictability. We show that HebEMO yields a high F1-score of 0.96 for polarity classification. Emotion detection reaches F1-scores of 0.78-0.97 for various target emotions, with the exception of surprise, which the model failed to capture (F1 = 0.41). These results are better than the best-reported performance, even among English-language models of emotion detection.

Vaccine hesitancy has been a common concern, probably since vaccines were created and, with the popularisation of social media, people started to express their concerns about vaccines online alongside those posting pro- and anti-vaccine content. Predictably, since the first mentions of a COVID-19 vaccine, social media users posted about their fears and concerns or about their support and belief into the effectiveness of these rapidly developing vaccines. Identifying and understanding the reasons behind public hesitancy towards COVID-19 vaccines is important for policy markers that need to develop actions to better inform the population with the aim of increasing vaccine take-up. In the case of COVID-19, where the fast development of the vaccines was mirrored closely by growth in anti-vaxx disinformation, automatic means of detecting citizen attitudes towards vaccination became necessary. This is an important computational social sciences task that requires data analysis in order to gain in-depth understanding of the phenomena at hand. Annotated data is also necessary for training data-driven models for more nuanced analysis of attitudes towards vaccination. To this end, we created a new collection of over 3,101 tweets annotated with users' attitudes towards COVID-19 vaccination (stance). Besides, we also develop a domain-specific language model (VaxxBERT) that achieves the best predictive performance (73.0 accuracy and 69.3 F1-score) as compared to a robust set of baselines. To the best of our knowledge, these are the first dataset and model that model vaccine hesitancy as a category distinct from pro- and anti-vaccine stance.

Along with the COVID-19 pandemic, an "infodemic" of false and misleading information has emerged and has complicated the COVID-19 response efforts. Social networking sites such as Facebook and Twitter have contributed largely to the spread of rumors, conspiracy theories, hate, xenophobia, racism, and prejudice. To combat the spread of fake news, researchers around the world have and are still making considerable efforts to build and share COVID-19 related research articles, models, and datasets. This paper releases "AraCOVID19-MFH" a manually annotated multi-label Arabic COVID-19 fake news and hate speech detection dataset. Our dataset contains 10,828 Arabic tweets annotated with 10 different labels. The labels have been designed to consider some aspects relevant to the fact-checking task, such as the tweet's check worthiness, positivity/negativity, and factuality. To confirm our annotated dataset's practical utility, we used it to train and evaluate several classification models and reported the obtained results. Though the dataset is mainly designed for fake news detection, it can also be used for hate speech detection, opinion/news classification, dialect identification, and many other tasks.

The 2019 coronavirus disease (COVID-19), emerged late December 2019 in China, is now rapidly spreading across the globe. At the time of writing this paper, the number of global confirmed cases has passed two millions and half with over 180,000 fatalities. Many countries have enforced strict social distancing policies to contain the spread of the virus. This have changed the daily life of tens of millions of people, and urged people to turn their discussions online, e.g., via online social media sites like Twitter. In this work, we describe the first Arabic tweets dataset on COVID-19 that we have been collecting since January 1st, 2020. The dataset would help researchers and policy makers in studying different societal issues related to the pandemic. Many other tasks related to behavioral change, information sharing, misinformation and rumors spreading can also be analyzed.

Coronavirus disease (COVID-19) is an infectious respiratory disease that was first discovered in late December 2019, in Wuhan, China, and then spread worldwide causing a lot of panic and death. Users of social networking sites such as Facebook and Twitter have been focused on reading, publishing, and sharing novelties, tweets, and articles regarding the newly emerging pandemic. A lot of these users often employ sarcasm to convey their intended meaning in a humorous, funny, and indirect way making it hard for computer-based applications to automatically understand and identify their goal and the harm level that they can inflect. Motivated by the emerging need for annotated datasets that tackle these kinds of problems in the context of COVID-19, this paper builds and releases AraCOVID19-SSD a manually annotated Arabic COVID-19 sarcasm and sentiment detection dataset containing 5,162 tweets. To confirm the practical utility of the built dataset, it has been carefully analyzed and tested using several classification models.

With the rapid development of COVID-19 into a global pandemic, there is an ever more urgent need for cheap, fast and reliable tools that can assist physicians in diagnosing COVID-19. Medical imaging such as CT can take a key role in complementing conventional diagnostic tools from molecular biology, and, using deep learning techniques, several automatic systems were demonstrated promising performances using CT or X-ray data. Here, we advocate a more prominent role of point-of-care ultrasound imaging to guide COVID-19 detection. Ultrasound is non-invasive and ubiquitous in medical facilities around the globe. Our contribution is threefold. First, we gather a lung ultrasound (POCUS) dataset consisting of 1103 images (654 COVID-19, 277 bacterial pneumonia and 172 healthy controls), sampled from 64 videos. This dataset was assembled from various online sources, processed specifically for deep learning models and is intended to serve as a starting point for an open-access initiative. Second, we train a deep convolutional neural network (POCOVID-Net) on this 3-class dataset and achieve an accuracy of 89% and, by a majority vote, a video accuracy of 92% . For detecting COVID-19 in particular, the model performs with a sensitivity of 0.96, a specificity of 0.79 and F1-score of 0.92 in a 5-fold cross validation. Third, we provide an open-access web service (POCOVIDScreen) that is available at: https://pocovidscreen.org. The website deploys the predictive model, allowing to perform predictions on ultrasound lung images. In addition, it grants medical staff the option to (bulk) upload their own screenings in order to contribute to the growing public database of pathological lung ultrasound images. Dataset and code are available from: https://github.com/jannisborn/covid19_pocus_ultrasound. NOTE: This preprint is superseded by our paper in Applied Sciences: https://doi.org/10.3390/app11020672

Rapid and affordable methods of testing for COVID-19 infections are essential to reduce infection rates and prevent medical facilities from becoming overwhelmed. Current approaches of detecting COVID-19 require in-person testing with expensive kits that are not always easily accessible. This study demonstrates that crowdsourced cough audio samples recorded and acquired on smartphones from around the world can be used to develop an AI-based method that accurately predicts COVID-19 infection with an ROC-AUC of 77.1% (75.2%-78.3%). Furthermore, we show that our method is able to generalize to crowdsourced audio samples from Latin America and clinical samples from South Asia, without further training using the specific samples from those regions. As more crowdsourced data is collected, further development can be implemented using various respiratory audio samples to create a cough analysis-based machine learning (ML) solution for COVID-19 detection that can likely generalize globally to all demographic groups in both clinical and non-clinical settings.

The past several years have witnessed a huge surge in the use of social media platforms during mass convergence events such as health emergencies, natural or human-induced disasters. These non-traditional data sources are becoming vital for disease forecasts and surveillance when preparing for epidemic and pandemic outbreaks. In this paper, we present GeoCoV19, a large-scale Twitter dataset containing more than 524 million multilingual tweets posted over a period of 90 days since February 1, 2020. Moreover, we employ a gazetteer-based approach to infer the geolocation of tweets. We postulate that this large-scale, multilingual, geolocated social media data can empower the research communities to evaluate how societies are collectively coping with this unprecedented global crisis as well as to develop computational methods to address challenges such as identifying fake news, understanding communities' knowledge gaps, building disease forecast and surveillance models, among others.

This paper introduces a multilingual dataset of COVID-19 vaccine misinformation, consisting of annotated tweets from three middle-income countries: Brazil, Indonesia, and Nigeria. The expertly curated dataset includes annotations for 5,952 tweets, assessing their relevance to COVID-19 vaccines, presence of misinformation, and the themes of the misinformation. To address challenges posed by domain specificity, the low-resource setting, and data imbalance, we adopt two approaches for developing COVID-19 vaccine misinformation detection models: domain-specific pre-training and text augmentation using a large language model. Our best misinformation detection models demonstrate improvements ranging from 2.7 to 15.9 percentage points in macro F1-score compared to the baseline models. Additionally, we apply our misinformation detection models in a large-scale study of 19 million unlabeled tweets from the three countries between 2020 and 2022, showcasing the practical application of our dataset and models for detecting and analyzing vaccine misinformation in multiple countries and languages. Our analysis indicates that percentage changes in the number of new COVID-19 cases are positively associated with COVID-19 vaccine misinformation rates in a staggered manner for Brazil and Indonesia, and there are significant positive associations between the misinformation rates across the three countries.

Controlling the COVID-19 pandemic largely hinges upon the existence of fast, safe, and highly-available diagnostic tools. Ultrasound, in contrast to CT or X-Ray, has many practical advantages and can serve as a globally-applicable first-line examination technique. We provide the largest publicly available lung ultrasound (US) dataset for COVID-19 consisting of 106 videos from three classes (COVID-19, bacterial pneumonia, and healthy controls); curated and approved by medical experts. On this dataset, we perform an in-depth study of the value of deep learning methods for differential diagnosis of COVID-19. We propose a frame-based convolutional neural network that correctly classifies COVID-19 US videos with a sensitivity of 0.98+-0.04 and a specificity of 0.91+-08 (frame-based sensitivity 0.93+-0.05, specificity 0.87+-0.07). We further employ class activation maps for the spatio-temporal localization of pulmonary biomarkers, which we subsequently validate for human-in-the-loop scenarios in a blindfolded study with medical experts. Aiming for scalability and robustness, we perform ablation studies comparing mobile-friendly, frame- and video-based architectures and show reliability of the best model by aleatoric and epistemic uncertainty estimates. We hope to pave the road for a community effort toward an accessible, efficient and interpretable screening method and we have started to work on a clinical validation of the proposed method. Data and code are publicly available.

The COVID-19 pandemic strained healthcare resources and prompted discussion about how machine learning can alleviate physician burdens and contribute to diagnosis. Chest x-rays (CXRs) are used for diagnosis of COVID-19, but few studies predict the severity of a patient's condition from CXRs. In this study, we produce a large COVID severity dataset by merging three sources and investigate the efficacy of transfer learning using ImageNet- and CXR-pretrained models and vision transformers (ViTs) in both severity regression and classification tasks. A pretrained DenseNet161 model performed the best on the three class severity prediction problem, reaching 80% accuracy overall and 77.3%, 83.9%, and 70% on mild, moderate and severe cases, respectively. The ViT had the best regression results, with a mean absolute error of 0.5676 compared to radiologist-predicted severity scores. The project's source code is publicly available.

Convincing people to get vaccinated against COVID-19 is a key societal challenge in the present times. As a first step towards this goal, many prior works have relied on social media analysis to understand the specific concerns that people have towards these vaccines, such as potential side-effects, ineffectiveness, political factors, and so on. Though there are datasets that broadly classify social media posts into Anti-vax and Pro-Vax labels, there is no dataset (to our knowledge) that labels social media posts according to the specific anti-vaccine concerns mentioned in the posts. In this paper, we have curated CAVES, the first large-scale dataset containing about 10k COVID-19 anti-vaccine tweets labelled into various specific anti-vaccine concerns in a multi-label setting. This is also the first multi-label classification dataset that provides explanations for each of the labels. Additionally, the dataset also provides class-wise summaries of all the tweets. We also perform preliminary experiments on the dataset and show that this is a very challenging dataset for multi-label explainable classification and tweet summarization, as is evident by the moderate scores achieved by some state-of-the-art models. Our dataset and codes are available at: https://github.com/sohampoddar26/caves-data

Billions of people across the globe have been using social media platforms in their local languages to voice their opinions about the various topics related to the COVID-19 pandemic. Several organizations, including the World Health Organization, have developed automated social media analysis tools that classify COVID-19-related tweets into various topics. However, these tools that help combat the pandemic are limited to very few languages, making several countries unable to take their benefit. While multi-lingual or low-resource language-specific tools are being developed, they still need to expand their coverage, such as for the Nepali language. In this paper, we identify the eight most common COVID-19 discussion topics among the Twitter community using the Nepali language, set up an online platform to automatically gather Nepali tweets containing the COVID-19-related keywords, classify the tweets into the eight topics, and visualize the results across the period in a web-based dashboard. We compare the performance of two state-of-the-art multi-lingual language models for Nepali tweet classification, one generic (mBERT) and the other Nepali language family-specific model (MuRIL). Our results show that the models' relative performance depends on the data size, with MuRIL doing better for a larger dataset. The annotated data, models, and the web-based dashboard are open-sourced at https://github.com/naamiinepal/covid-tweet-classification.

The spread of COVID-19 has sparked racism and hate on social media targeted towards Asian communities. However, little is known about how racial hate spreads during a pandemic and the role of counterspeech in mitigating this spread. In this work, we study the evolution and spread of anti-Asian hate speech through the lens of Twitter. We create COVID-HATE, the largest dataset of anti-Asian hate and counterspeech spanning 14 months, containing over 206 million tweets, and a social network with over 127 million nodes. By creating a novel hand-labeled dataset of 3,355 tweets, we train a text classifier to identify hate and counterspeech tweets that achieves an average macro-F1 score of 0.832. Using this dataset, we conduct longitudinal analysis of tweets and users. Analysis of the social network reveals that hateful and counterspeech users interact and engage extensively with one another, instead of living in isolated polarized communities. We find that nodes were highly likely to become hateful after being exposed to hateful content. Notably, counterspeech messages may discourage users from turning hateful, potentially suggesting a solution to curb hate on web and social media platforms. Data and code is at http://claws.cc.gatech.edu/covid.

As of writing this paper, COVID-19 (Coronavirus disease 2019) has spread to more than 220 countries and territories. Following the outbreak, the pandemic's seriousness has made people more active on social media, especially on the microblogging platforms such as Twitter and Weibo. The pandemic-specific discourse has remained on-trend on these platforms for months now. Previous studies have confirmed the contributions of such socially generated conversations towards situational awareness of crisis events. The early forecasts of cases are essential to authorities to estimate the requirements of resources needed to cope with the outgrowths of the virus. Therefore, this study attempts to incorporate the public discourse in the design of forecasting models particularly targeted for the steep-hill region of an ongoing wave. We propose a sentiment-involved topic-based latent variables search methodology for designing forecasting models from publicly available Twitter conversations. As a use case, we implement the proposed methodology on Australian COVID-19 daily cases and Twitter conversations generated within the country. Experimental results: (i) show the presence of latent social media variables that Granger-cause the daily COVID-19 confirmed cases, and (ii) confirm that those variables offer additional prediction capability to forecasting models. Further, the results show that the inclusion of social media variables introduces 48.83--51.38% improvements on RMSE over the baseline models. We also release the large-scale COVID-19 specific geotagged global tweets dataset, MegaGeoCOV, to the public anticipating that the geotagged data of this scale would aid in understanding the conversational dynamics of the pandemic through other spatial and temporal contexts.

The COVID-19 pandemic has made a huge global impact and cost millions of lives. As COVID-19 vaccines were rolled out, they were quickly met with widespread hesitancy. To address the concerns of hesitant people, we launched VIRA, a public dialogue system aimed at addressing questions and concerns surrounding the COVID-19 vaccines. Here, we release VIRADialogs, a dataset of over 8k dialogues conducted by actual users with VIRA, providing a unique real-world conversational dataset. In light of rapid changes in users' intents, due to updates in guidelines or in response to new information, we highlight the important task of intent discovery in this use-case. We introduce a novel automatic evaluation framework for intent discovery, leveraging the existing intent classifier of VIRA. We use this framework to report baseline intent discovery results over VIRADialogs, that highlight the difficulty of this task.

The spread of online misinformation threatens public health, democracy, and the broader society. While professional fact-checkers form the first line of defense by fact-checking popular false claims, they do not engage directly in conversations with misinformation spreaders. On the other hand, non-expert ordinary users act as eyes-on-the-ground who proactively counter misinformation -- recent research has shown that 96% counter-misinformation responses are made by ordinary users. However, research also found that 2/3 times, these responses are rude and lack evidence. This work seeks to create a counter-misinformation response generation model to empower users to effectively correct misinformation. This objective is challenging due to the absence of datasets containing ground-truth of ideal counter-misinformation responses, and the lack of models that can generate responses backed by communication theories. In this work, we create two novel datasets of misinformation and counter-misinformation response pairs from in-the-wild social media and crowdsourcing from college-educated students. We annotate the collected data to distinguish poor from ideal responses that are factual, polite, and refute misinformation. We propose MisinfoCorrect, a reinforcement learning-based framework that learns to generate counter-misinformation responses for an input misinformation post. The model rewards the generator to increase the politeness, factuality, and refutation attitude while retaining text fluency and relevancy. Quantitative and qualitative evaluation shows that our model outperforms several baselines by generating high-quality counter-responses. This work illustrates the promise of generative text models for social good -- here, to help create a safe and reliable information ecosystem. The code and data is accessible on https://github.com/claws-lab/MisinfoCorrect.

A molecular and cellular understanding of how SARS-CoV-2 variably infects and causes severe COVID-19 remains a bottleneck in developing interventions to end the pandemic. We sought to use deep learning to study the biology of SARS-CoV-2 infection and COVID-19 severity by identifying transcriptomic patterns and cell types associated with SARS-CoV-2 infection and COVID-19 severity. To do this, we developed a new approach to generating self-supervised edge features. We propose a model that builds on Graph Attention Networks (GAT), creates edge features using self-supervised learning, and ingests these edge features via a Set Transformer. This model achieves significant improvements in predicting the disease state of individual cells, given their transcriptome. We apply our model to single-cell RNA sequencing datasets of SARS-CoV-2 infected lung organoids and bronchoalveolar lavage fluid samples of patients with COVID-19, achieving state-of-the-art performance on both datasets with our model. We then borrow from the field of explainable AI (XAI) to identify the features (genes) and cell types that discriminate bystander vs. infected cells across time and moderate vs. severe COVID-19 disease. To the best of our knowledge, this represents the first application of deep learning to identifying the molecular and cellular determinants of SARS-CoV-2 infection and COVID-19 severity using single-cell omics data.

In this work, we release COVID-Twitter-BERT (CT-BERT), a transformer-based model, pretrained on a large corpus of Twitter messages on the topic of COVID-19. Our model shows a 10-30% marginal improvement compared to its base model, BERT-Large, on five different classification datasets. The largest improvements are on the target domain. Pretrained transformer models, such as CT-BERT, are trained on a specific target domain and can be used for a wide variety of natural language processing tasks, including classification, question-answering and chatbots. CT-BERT is optimised to be used on COVID-19 content, in particular social media posts from Twitter.

The COVID-19 pandemic has been severely impacting global society since December 2019. Massive research has been undertaken to understand the characteristics of the virus and design vaccines and drugs. The related findings have been reported in biomedical literature at a rate of about 10,000 articles on COVID-19 per month. Such rapid growth significantly challenges manual curation and interpretation. For instance, LitCovid is a literature database of COVID-19-related articles in PubMed, which has accumulated more than 200,000 articles with millions of accesses each month by users worldwide. One primary curation task is to assign up to eight topics (e.g., Diagnosis and Treatment) to the articles in LitCovid. Despite the continuing advances in biomedical text mining methods, few have been dedicated to topic annotations in COVID-19 literature. To close the gap, we organized the BioCreative LitCovid track to call for a community effort to tackle automated topic annotation for COVID-19 literature. The BioCreative LitCovid dataset, consisting of over 30,000 articles with manually reviewed topics, was created for training and testing. It is one of the largest multilabel classification datasets in biomedical scientific literature. 19 teams worldwide participated and made 80 submissions in total. Most teams used hybrid systems based on transformers. The highest performing submissions achieved 0.8875, 0.9181, and 0.9394 for macro F1-score, micro F1-score, and instance-based F1-score, respectively. The level of participation and results demonstrate a successful track and help close the gap between dataset curation and method development. The dataset is publicly available via https://ftp.ncbi.nlm.nih.gov/pub/lu/LitCovid/biocreative/ for benchmarking and further development.

COVID-19 (coronavirus disease 2019) pandemic caused by SARS-CoV-2 has led to a treacherous and devastating catastrophe for humanity. At the time of writing, no specific antivirus drugs or vaccines are recommended to control infection transmission and spread. The current diagnosis of COVID-19 is done by Reverse-Transcription Polymer Chain Reaction (RT-PCR) testing. However, this method is expensive, time-consuming, and not easily available in straitened regions. An interpretable and COVID-19 diagnosis AI framework is devised and developed based on the cough sounds features and symptoms metadata to overcome these limitations. The proposed framework's performance was evaluated using a medical dataset containing Symptoms and Demographic data of 30000 audio segments, 328 cough sounds from 150 patients with four cough classes ( COVID-19, Asthma, Bronchitis, and Healthy). Experiments' results show that the model captures the better and robust feature embedding to distinguish between COVID-19 patient coughs and several types of non-COVID-19 coughs with higher specificity and accuracy of 95.04 pm 0.18% and 96.83pm 0.18% respectively, all the while maintaining interpretability.

Fact checking by professionals is viewed as a vital defense in the fight against misinformation.While fact checking is important and its impact has been significant, fact checks could have limited visibility and may not reach the intended audience, such as those deeply embedded in polarized communities. Concerned citizens (i.e., the crowd), who are users of the platforms where misinformation appears, can play a crucial role in disseminating fact-checking information and in countering the spread of misinformation. To explore if this is the case, we conduct a data-driven study of misinformation on the Twitter platform, focusing on tweets related to the COVID-19 pandemic, analyzing the spread of misinformation, professional fact checks, and the crowd response to popular misleading claims about COVID-19. In this work, we curate a dataset of false claims and statements that seek to challenge or refute them. We train a classifier to create a novel dataset of 155,468 COVID-19-related tweets, containing 33,237 false claims and 33,413 refuting arguments.Our findings show that professional fact-checking tweets have limited volume and reach. In contrast, we observe that the surge in misinformation tweets results in a quick response and a corresponding increase in tweets that refute such misinformation. More importantly, we find contrasting differences in the way the crowd refutes tweets, some tweets appear to be opinions, while others contain concrete evidence, such as a link to a reputed source. Our work provides insights into how misinformation is organically countered in social platforms by some of their users and the role they play in amplifying professional fact checks.These insights could lead to development of tools and mechanisms that can empower concerned citizens in combating misinformation. The code and data can be found in http://claws.cc.gatech.edu/covid_counter_misinformation.html.

Over the course of the COVID-19 pandemic, large volumes of biomedical information concerning this new disease have been published on social media. Some of this information can pose a real danger to people's health, particularly when false information is shared, for instance recommendations on how to treat diseases without professional medical advice. Therefore, automatic fact-checking resources and systems developed specifically for the medical domain are crucial. While existing fact-checking resources cover COVID-19-related information in news or quantify the amount of misinformation in tweets, there is no dataset providing fact-checked COVID-19-related Twitter posts with detailed annotations for biomedical entities, relations and relevant evidence. We contribute CoVERT, a fact-checked corpus of tweets with a focus on the domain of biomedicine and COVID-19-related (mis)information. The corpus consists of 300 tweets, each annotated with medical named entities and relations. We employ a novel crowdsourcing methodology to annotate all tweets with fact-checking labels and supporting evidence, which crowdworkers search for online. This methodology results in moderate inter-annotator agreement. Furthermore, we use the retrieved evidence extracts as part of a fact-checking pipeline, finding that the real-world evidence is more useful than the knowledge indirectly available in pretrained language models.

The rapid and accurate detection of COVID-19 cases is critical for timely treatment and preventing the spread of the disease. In this study, a two-stage feature extraction framework using eight state-of-the-art pre-trained deep Convolutional Neural Networks (CNNs) and an autoencoder is proposed to determine the health conditions of patients (COVID-19, Normal, Viral Pneumonia) based on chest X-rays. The X-ray scans are divided into four equally sized sections and analyzed by deep pre-trained CNNs. Subsequently, an autoencoder with three hidden layers is trained to extract reproductive features from the concatenated ouput of CNNs. To evaluate the performance of the proposed framework, three different classifiers, which are single-layer perceptron (SLP), multi-layer perceptron (MLP), and support vector machine (SVM) are used. Furthermore, the deep CNN architectures are used to create benchmark models and trained on the same dataset for comparision. The proposed framework outperforms other frameworks wih pre-trained feature extractors in binary classification and shows competitive results in three-class classification. The proposed methodology is task-independent and suitable for addressing various problems. The results show that the discriminative features are a subset of the reproductive features, suggesting that extracting task-independent features is superior to the extraction only task-based features. The flexibility and task-independence of the reproductive features make the conceptive information approach more favorable. The proposed methodology is novel and shows promising results for analyzing medical image data.

The COVID-19 pandemic presents global challenges transcending boundaries of country, race, religion, and economy. The current gold standard method for COVID-19 detection is the reverse transcription polymerase chain reaction (RT-PCR) testing. However, this method is expensive, time-consuming, and violates social distancing. Also, as the pandemic is expected to stay for a while, there is a need for an alternate diagnosis tool which overcomes these limitations, and is deployable at a large scale. The prominent symptoms of COVID-19 include cough and breathing difficulties. We foresee that respiratory sounds, when analyzed using machine learning techniques, can provide useful insights, enabling the design of a diagnostic tool. Towards this, the paper presents an early effort in creating (and analyzing) a database, called Coswara, of respiratory sounds, namely, cough, breath, and voice. The sound samples are collected via worldwide crowdsourcing using a website application. The curated dataset is released as open access. As the pandemic is evolving, the data collection and analysis is a work in progress. We believe that insights from analysis of Coswara can be effective in enabling sound based technology solutions for point-of-care diagnosis of respiratory infection, and in the near future this can help to diagnose COVID-19.

Despite being an integral tool for finding health-related information online, YouTube has faced criticism for disseminating COVID-19 misinformation globally to its users. Yet, prior audit studies have predominantly investigated YouTube within the Global North contexts, often overlooking the Global South. To address this gap, we conducted a comprehensive 10-day geolocation-based audit on YouTube to compare the prevalence of COVID-19 misinformation in search results between the United States (US) and South Africa (SA), the countries heavily affected by the pandemic in the Global North and the Global South, respectively. For each country, we selected 3 geolocations and placed sock-puppets, or bots emulating "real" users, that collected search results for 48 search queries sorted by 4 search filters for 10 days, yielding a dataset of 915K results. We found that 31.55% of the top-10 search results contained COVID-19 misinformation. Among the top-10 search results, bots in SA faced significantly more misinformative search results than their US counterparts. Overall, our study highlights the contrasting algorithmic behaviors of YouTube search between two countries, underscoring the need for the platform to regulate algorithmic behavior consistently across different regions of the Globe.

Loneliness has been associated with negative outcomes for physical and mental health. Understanding how people express and cope with various forms of loneliness is critical for early screening and targeted interventions to reduce loneliness, particularly among vulnerable groups such as young adults. To examine how different forms of loneliness and coping strategies manifest in loneliness self-disclosure, we built a dataset, FIG-Loneliness (FIne-Grained Loneliness) by using Reddit posts in two young adult-focused forums and two loneliness related forums consisting of a diverse age group. We provided annotations by trained human annotators for binary and fine-grained loneliness classifications of the posts. Trained on FIG-Loneliness, two BERT-based models were used to understand loneliness forms and authors' coping strategies in these forums. Our binary loneliness classification achieved an accuracy above 97%, and fine-grained loneliness category classification reached an average accuracy of 77% across all labeled categories. With FIG-Loneliness and model predictions, we found that loneliness expressions in the young adults related forums were distinct from other forums. Those in young adult-focused forums were more likely to express concerns pertaining to peer relationship, and were potentially more sensitive to geographical isolation impacted by the COVID-19 pandemic lockdown. Also, we showed that different forms of loneliness have differential use in coping strategies.

Background: This study aimed to evaluate and compare the performance of classical machine learning models (CMLs) and large language models (LLMs) in predicting mortality associated with COVID-19 by utilizing a high-dimensional tabular dataset. Materials and Methods: We analyzed data from 9,134 COVID-19 patients collected across four hospitals. Seven CML models, including XGBoost and random forest (RF), were trained and evaluated. The structured data was converted into text for zero-shot classification by eight LLMs, including GPT-4 and Mistral-7b. Additionally, Mistral-7b was fine-tuned using the QLoRA approach to enhance its predictive capabilities. Results: Among the CML models, XGBoost and RF achieved the highest accuracy, with F1 scores of 0.87 for internal validation and 0.83 for external validation. In the LLM category, GPT-4 was the top performer with an F1 score of 0.43. Fine-tuning Mistral-7b significantly improved its recall from 1% to 79%, resulting in an F1 score of 0.74, which was stable during external validation. Conclusion: While LLMs show moderate performance in zero-shot classification, fine-tuning can significantly enhance their effectiveness, potentially aligning them closer to CML models. However, CMLs still outperform LLMs in high-dimensional tabular data tasks.

The global outbreak of the Coronavirus 2019 (COVID-19) has overloaded worldwide healthcare systems. Computer-aided diagnosis for COVID-19 fast detection and patient triage is becoming critical. This paper proposes a novel self-knowledge distillation based self-supervised learning method for COVID-19 detection from chest X-ray images. Our method can use self-knowledge of images based on similarities of their visual features for self-supervised learning. Experimental results show that our method achieved an HM score of 0.988, an AUC of 0.999, and an accuracy of 0.957 on the largest open COVID-19 chest X-ray dataset.

Misinformation spread in online social networks is an urgent-to-solve problem having harmful consequences that threaten human health, public safety, economics, and so on. In this study, we construct a novel dataset, called MiDe-22, having 5,284 English and 5,064 Turkish tweets with their misinformation labels under several recent events, including the Russia-Ukraine war, COVID-19 pandemic, and Refugees. Moreover, we provide the user engagements to the tweets in terms of likes, replies, retweets, and quotes. We present a detailed data analysis with descriptive statistics and temporal analysis, and provide the experimental results of a benchmark evaluation for misinformation detection on our novel dataset.

The pervasive influence of misinformation has far-reaching and detrimental effects on both individuals and society. The COVID-19 pandemic has witnessed an alarming surge in the dissemination of medical misinformation. However, existing datasets pertaining to misinformation predominantly focus on textual information, neglecting the inclusion of visual elements, and tend to center solely on COVID-19-related misinformation, overlooking misinformation surrounding other diseases. Furthermore, the potential of Large Language Models (LLMs), such as the ChatGPT developed in late 2022, in generating misinformation has been overlooked in previous works. To overcome these limitations, we present Med-MMHL, a novel multi-modal misinformation detection dataset in a general medical domain encompassing multiple diseases. Med-MMHL not only incorporates human-generated misinformation but also includes misinformation generated by LLMs like ChatGPT. Our dataset aims to facilitate comprehensive research and development of methodologies for detecting misinformation across diverse diseases and various scenarios, including human and LLM-generated misinformation detection at the sentence, document, and multi-modal levels. To access our dataset and code, visit our GitHub repository: https://github.com/styxsys0927/Med-MMHL.

Recently, due to COVID-19 and the growing demand for remote work, video conferencing apps have become especially widespread. The most valuable features of video chats are real-time background removal and face beautification. While solving these tasks, computer vision researchers face the problem of having relevant data for the training stage. There is no large dataset with high-quality labeled and diverse images of people in front of a laptop or smartphone camera to train a lightweight model without additional approaches. To boost the progress in this area, we provide a new image dataset, EasyPortrait, for portrait segmentation and face parsing tasks. It contains 20,000 primarily indoor photos of 8,377 unique users, and fine-grained segmentation masks separated into 9 classes. Images are collected and labeled from crowdsourcing platforms. Unlike most face parsing datasets, in EasyPortrait, the beard is not considered part of the skin mask, and the inside area of the mouth is separated from the teeth. These features allow using EasyPortrait for skin enhancement and teeth whitening tasks. This paper describes the pipeline for creating a large-scale and clean image segmentation dataset using crowdsourcing platforms without additional synthetic data. Moreover, we trained several models on EasyPortrait and showed experimental results. Proposed dataset and trained models are publicly available.

The World Health Organization added Disease X to their shortlist of blueprint priority diseases to represent a hypothetical, unknown pathogen that could cause a future epidemic. During different virus outbreaks of the past, such as COVID-19, Influenza, Lyme Disease, and Zika virus, researchers from various disciplines utilized Google Trends to mine multimodal components of web behavior to study, investigate, and analyze the global awareness, preparedness, and response associated with these respective virus outbreaks. As the world prepares for Disease X, a dataset on web behavior related to Disease X would be crucial to contribute towards the timely advancement of research in this field. Furthermore, none of the prior works in this field have focused on the development of a dataset to compile relevant web behavior data, which would help to prepare for Disease X. To address these research challenges, this work presents a dataset of web behavior related to Disease X, which emerged from different geographic regions of the world, between February 2018 and August 2023. Specifically, this dataset presents the search interests related to Disease X from 94 geographic regions. The dataset was developed by collecting data using Google Trends. The relevant search interests for all these regions for each month in this time range are available in this dataset. This paper also discusses the compliance of this dataset with the FAIR principles of scientific data management. Finally, an analysis of this dataset is presented to uphold the applicability, relevance, and usefulness of this dataset for the investigation of different research questions in the interrelated fields of Big Data, Data Mining, Healthcare, Epidemiology, and Data Analysis with a specific focus on Disease X.

As a lightweight and non-invasive imaging technique, lung ultrasound (LUS) has gained importance for assessing lung pathologies. The use of Artificial intelligence (AI) in medical decision support systems is promising due to the time- and expertise-intensive interpretation, however, due to the poor quality of existing data used for training AI models, their usability for real-world applications remains unclear. In a prospective study, we analyze data from 63 COVID-19 suspects (33 positive) collected at Maastricht University Medical Centre. Ultrasound recordings at six body locations were acquired following the BLUE protocol and manually labeled for severity of lung involvement. Several AI models were applied and trained for detection and severity of pulmonary infection. The severity of the lung infection, as assigned by human annotators based on the LUS videos, is not significantly different between COVID-19 positive and negative patients (p = 0.89). Nevertheless, the predictions of image-based AI models identify a COVID-19 infection with 65% accuracy when applied zero-shot (i.e., trained on other datasets), and up to 79% with targeted training, whereas the accuracy based on human annotations is at most 65%. Multi-modal models combining images and CBC improve significantly over image-only models. Although our analysis generally supports the value of AI in LUS assessment, the evaluated models fall short of the performance expected from previous work. We find this is due to 1) the heterogeneity of LUS datasets, limiting the generalization ability to new data, 2) the frame-based processing of AI models ignoring video-level information, and 3) lack of work on multi-modal models that can extract the most relevant information from video-, image- and variable-based inputs. To aid future research, we publish the dataset at: https://github.com/NinaWie/COVID-BLUES.

In recent years, the problem of misinformation on the web has become widespread across languages, countries, and various social media platforms. Although there has been much work on automated fake news detection, the role of images and their variety are not well explored. In this paper, we investigate the roles of image and text at an earlier stage of the fake news detection pipeline, called claim detection. For this purpose, we introduce a novel dataset, MM-Claims, which consists of tweets and corresponding images over three topics: COVID-19, Climate Change and broadly Technology. The dataset contains roughly 86000 tweets, out of which 3400 are labeled manually by multiple annotators for the training and evaluation of multimodal models. We describe the dataset in detail, evaluate strong unimodal and multimodal baselines, and analyze the potential and drawbacks of current models.

Retrieval Augment Generation (RAG) is a recent advancement in Open-Domain Question Answering (ODQA). RAG has only been trained and explored with a Wikipedia-based external knowledge base and is not optimized for use in other specialized domains such as healthcare and news. In this paper, we evaluate the impact of joint training of the retriever and generator components of RAG for the task of domain adaptation in ODQA. We propose RAG-end2end, an extension to RAG, that can adapt to a domain-specific knowledge base by updating all components of the external knowledge base during training. In addition, we introduce an auxiliary training signal to inject more domain-specific knowledge. This auxiliary signal forces RAG-end2end to reconstruct a given sentence by accessing the relevant information from the external knowledge base. Our novel contribution is unlike RAG, RAG-end2end does joint training of the retriever and generator for the end QA task and domain adaptation. We evaluate our approach with datasets from three domains: COVID-19, News, and Conversations, and achieve significant performance improvements compared to the original RAG model. Our work has been open-sourced through the Huggingface Transformers library, attesting to our work's credibility and technical consistency.

Forecasting future world events is a challenging but valuable task. Forecasts of climate, geopolitical conflict, pandemics and economic indicators help shape policy and decision making. In these domains, the judgment of expert humans contributes to the best forecasts. Given advances in language modeling, can these forecasts be automated? To this end, we introduce Autocast, a dataset containing thousands of forecasting questions and an accompanying news corpus. Questions are taken from forecasting tournaments, ensuring high quality, real-world importance, and diversity. The news corpus is organized by date, allowing us to precisely simulate the conditions under which humans made past forecasts (avoiding leakage from the future). Motivated by the difficulty of forecasting numbers across orders of magnitude (e.g. global cases of COVID-19 in 2022), we also curate IntervalQA, a dataset of numerical questions and metrics for calibration. We test language models on our forecasting task and find that performance is far below a human expert baseline. However, performance improves with increased model size and incorporation of relevant information from the news corpus. In sum, Autocast poses a novel challenge for large language models and improved performance could bring large practical benefits.

The way people respond to messaging from public health organizations on social media can provide insight into public perceptions on critical health issues, especially during a global crisis such as COVID-19. It could be valuable for high-impact organizations such as the US Centers for Disease Control and Prevention (CDC) or the World Health Organization (WHO) to understand how these perceptions impact reception of messaging on health policy recommendations. We collect two datasets of public health messages and their responses from Twitter relating to COVID-19 and Vaccines, and introduce a predictive method which can be used to explore the potential reception of such messages. Specifically, we harness a generative model (GPT-2) to directly predict probable future responses and demonstrate how it can be used to optimize expected reception of important health guidance. Finally, we introduce a novel evaluation scheme with extensive statistical testing which allows us to conclude that our models capture the semantics and sentiment found in actual public health responses.

We introduce scientific claim verification, a new task to select abstracts from the research literature containing evidence that SUPPORTS or REFUTES a given scientific claim, and to identify rationales justifying each decision. To study this task, we construct SciFact, a dataset of 1.4K expert-written scientific claims paired with evidence-containing abstracts annotated with labels and rationales. We develop baseline models for SciFact, and demonstrate that simple domain adaptation techniques substantially improve performance compared to models trained on Wikipedia or political news. We show that our system is able to verify claims related to COVID-19 by identifying evidence from the CORD-19 corpus. Our experiments indicate that SciFact will provide a challenging testbed for the development of new systems designed to retrieve and reason over corpora containing specialized domain knowledge. Data and code for this new task are publicly available at https://github.com/allenai/scifact. A leaderboard and COVID-19 fact-checking demo are available at https://scifact.apps.allenai.org.

Accurate classification of computed tomography (CT) images is essential for diagnosis and treatment planning, but existing methods often struggle with the subtle and spatially diverse nature of pathological features. Current approaches typically process images uniformly, limiting their ability to detect localized abnormalities that require focused analysis. We introduce UGPL, an uncertainty-guided progressive learning framework that performs a global-to-local analysis by first identifying regions of diagnostic ambiguity and then conducting detailed examination of these critical areas. Our approach employs evidential deep learning to quantify predictive uncertainty, guiding the extraction of informative patches through a non-maximum suppression mechanism that maintains spatial diversity. This progressive refinement strategy, combined with an adaptive fusion mechanism, enables UGPL to integrate both contextual information and fine-grained details. Experiments across three CT datasets demonstrate that UGPL consistently outperforms state-of-the-art methods, achieving improvements of 3.29%, 2.46%, and 8.08% in accuracy for kidney abnormality, lung cancer, and COVID-19 detection, respectively. Our analysis shows that the uncertainty-guided component provides substantial benefits, with performance dramatically increasing when the full progressive learning pipeline is implemented. Our code is available at: https://github.com/shravan-18/UGPL

The proliferation of online misinformation has posed significant threats to public interest. While numerous online users actively participate in the combat against misinformation, many of such responses can be characterized by the lack of politeness and supporting facts. As a solution, text generation approaches are proposed to automatically produce counter-misinformation responses. Nevertheless, existing methods are often trained end-to-end without leveraging external knowledge, resulting in subpar text quality and excessively repetitive responses. In this paper, we propose retrieval augmented response generation for online misinformation (RARG), which collects supporting evidence from scientific sources and generates counter-misinformation responses based on the evidences. In particular, our RARG consists of two stages: (1) evidence collection, where we design a retrieval pipeline to retrieve and rerank evidence documents using a database comprising over 1M academic articles; (2) response generation, in which we align large language models (LLMs) to generate evidence-based responses via reinforcement learning from human feedback (RLHF). We propose a reward function to maximize the utilization of the retrieved evidence while maintaining the quality of the generated text, which yields polite and factual responses that clearly refutes misinformation. To demonstrate the effectiveness of our method, we study the case of COVID-19 and perform extensive experiments with both in- and cross-domain datasets, where RARG consistently outperforms baselines by generating high-quality counter-misinformation responses.

Synthetic data generation has the potential to impact applications and domains with scarce data. However, before such data is used for sensitive tasks such as mental health, we need an understanding of how different demographics are represented in it. In our paper, we analyze the potential of producing synthetic data using GPT-3 by exploring the various stressors it attributes to different race and gender combinations, to provide insight for future researchers looking into using LLMs for data generation. Using GPT-3, we develop HEADROOM, a synthetic dataset of 3,120 posts about depression-triggering stressors, by controlling for race, gender, and time frame (before and after COVID-19). Using this dataset, we conduct semantic and lexical analyses to (1) identify the predominant stressors for each demographic group; and (2) compare our synthetic data to a human-generated dataset. We present the procedures to generate queries to develop depression data using GPT-3, and conduct analyzes to uncover the types of stressors it assigns to demographic groups, which could be used to test the limitations of LLMs for synthetic data generation for depression data. Our findings show that synthetic data mimics some of the human-generated data distribution for the predominant depression stressors across diverse demographics.

Unsupervised anomaly detection (UAD) aims to find anomalous images by optimising a detector using a training set that contains only normal images. UAD approaches can be based on reconstruction methods, self-supervised approaches, and Imagenet pre-trained models. Reconstruction methods, which detect anomalies from image reconstruction errors, are advantageous because they do not rely on the design of problem-specific pretext tasks needed by self-supervised approaches, and on the unreliable translation of models pre-trained from non-medical datasets. However, reconstruction methods may fail because they can have low reconstruction errors even for anomalous images. In this paper, we introduce a new reconstruction-based UAD approach that addresses this low-reconstruction error issue for anomalous images. Our UAD approach, the memory-augmented multi-level cross-attentional masked autoencoder (MemMC-MAE), is a transformer-based approach, consisting of a novel memory-augmented self-attention operator for the encoder and a new multi-level cross-attention operator for the decoder. MemMCMAE masks large parts of the input image during its reconstruction, reducing the risk that it will produce low reconstruction errors because anomalies are likely to be masked and cannot be reconstructed. However, when the anomaly is not masked, then the normal patterns stored in the encoder's memory combined with the decoder's multi-level cross attention will constrain the accurate reconstruction of the anomaly. We show that our method achieves SOTA anomaly detection and localisation on colonoscopy, pneumonia, and covid-19 chest x-ray datasets.

The paper presents an open-domain Question Answering system for Romanian, answering COVID-19 related questions. The QA system pipeline involves automatic question processing, automatic query generation, web searching for the top 10 most relevant documents and answer extraction using a fine-tuned BERT model for Extractive QA, trained on a COVID-19 data set that we have manually created. The paper will present the QA system and its integration with the Romanian language technologies portal RELATE, the COVID-19 data set and different evaluations of the QA performance.

Coronavirus disease (COVID-19) is a pandemic disease, which has already caused thousands of causalities and infected several millions of people worldwide. Any technological tool enabling rapid screening of the COVID-19 infection with high accuracy can be crucially helpful to healthcare professionals. The main clinical tool currently in use for the diagnosis of COVID-19 is the Reverse transcription polymerase chain reaction (RT-PCR), which is expensive, less-sensitive and requires specialized medical personnel. X-ray imaging is an easily accessible tool that can be an excellent alternative in the COVID-19 diagnosis. This research was taken to investigate the utility of artificial intelligence (AI) in the rapid and accurate detection of COVID-19 from chest X-ray images. The aim of this paper is to propose a robust technique for automatic detection of COVID-19 pneumonia from digital chest X-ray images applying pre-trained deep-learning algorithms while maximizing the detection accuracy. A public database was created by the authors combining several public databases and also by collecting images from recently published articles. The database contains a mixture of 423 COVID-19, 1485 viral pneumonia, and 1579 normal chest X-ray images. Transfer learning technique was used with the help of image augmentation to train and validate several pre-trained deep Convolutional Neural Networks (CNNs). The networks were trained to classify two different schemes: i) normal and COVID-19 pneumonia; ii) normal, viral and COVID-19 pneumonia with and without image augmentation. The classification accuracy, precision, sensitivity, and specificity for both the schemes were 99.7%, 99.7%, 99.7% and 99.55% and 97.9%, 97.95%, 97.9%, and 98.8%, respectively.

The field of Explainable Artificial Intelligence (XAI) aims to build explainable and interpretable machine learning (or deep learning) methods without sacrificing prediction performance. Convolutional Neural Networks (CNNs) have been successful in making predictions, especially in image classification. However, these famous deep learning models use tens of millions of parameters based on a large number of pre-trained filters which have been repurposed from previous data sets. We propose a novel Interaction-based Convolutional Neural Network (ICNN) that does not make assumptions about the relevance of local information. Instead, we use a model-free Influence Score (I-score) to directly extract the influential information from images to form important variable modules. We demonstrate that the proposed method produces state-of-the-art prediction performance of 99.8% on a real-world data set classifying COVID-19 Chest X-ray images without sacrificing the explanatory power of the model. This proposed design can efficiently screen COVID-19 patients before human diagnosis, and will be the benchmark for addressing future XAI problems in large-scale data sets.

We present an overview of the TREC-COVID Challenge, an information retrieval (IR) shared task to evaluate search on scientific literature related to COVID-19. The goals of TREC-COVID include the construction of a pandemic search test collection and the evaluation of IR methods for COVID-19. The challenge was conducted over five rounds from April to July, 2020, with participation from 92 unique teams and 556 individual submissions. A total of 50 topics (sets of related queries) were used in the evaluation, starting at 30 topics for Round 1 and adding 5 new topics per round to target emerging topics at that state of the still-emerging pandemic. This paper provides a comprehensive overview of the structure and results of TREC-COVID. Specifically, the paper provides details on the background, task structure, topic structure, corpus, participation, pooling, assessment, judgments, results, top-performing systems, lessons learned, and benchmark datasets.

With worldwide concerns surrounding the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), there is a rapidly growing body of scientific literature on the virus. Clinicians, researchers, and policy-makers need to be able to search these articles effectively. In this work, we present a zero-shot ranking algorithm that adapts to COVID-related scientific literature. Our approach filters training data from another collection down to medical-related queries, uses a neural re-ranking model pre-trained on scientific text (SciBERT), and filters the target document collection. This approach ranks top among zero-shot methods on the TREC COVID Round 1 leaderboard, and exhibits a P@5 of 0.80 and an nDCG@10 of 0.68 when evaluated on both Round 1 and 2 judgments. Despite not relying on TREC-COVID data, our method outperforms models that do. As one of the first search methods to thoroughly evaluate COVID-19 search, we hope that this serves as a strong baseline and helps in the global crisis.

In the light of the COVID-19 pandemic, deep learning methods have been widely investigated in detecting COVID-19 from chest X-rays. However, a more pragmatic approach to applying AI methods to a medical diagnosis is designing a framework that facilitates human-machine interaction and expert decision making. Studies have shown that categorization can play an essential rule in accelerating real-world decision making. Inspired by descriptive document clustering, we propose a domain-independent explanatory clustering framework to group contextually related instances and support radiologists' decision making. While most descriptive clustering approaches employ domain-specific characteristics to form meaningful clusters, we focus on model-level explanation as a more general-purpose element of every learning process to achieve cluster homogeneity. We employ DeepSHAP to generate homogeneous clusters in terms of disease severity and describe the clusters using favorable and unfavorable saliency maps, which visualize the class discriminating regions of an image. These human-interpretable maps complement radiologist knowledge to investigate the whole cluster at once. Besides, as part of this study, we evaluate a model based on VGG-19, which can identify COVID and pneumonia cases with a positive predictive value of 95% and 97%, respectively, comparable to the recent explainable approaches for COVID diagnosis.

The COVID-19 pandemic swept across the world rapidly, infecting millions of people. An efficient tool that can accurately recognize important clinical concepts of COVID-19 from free text in electronic health records (EHRs) will be valuable to accelerate COVID-19 clinical research. To this end, this study aims at adapting the existing CLAMP natural language processing tool to quickly build COVID-19 SignSym, which can extract COVID-19 signs/symptoms and their 8 attributes (body location, severity, temporal expression, subject, condition, uncertainty, negation, and course) from clinical text. The extracted information is also mapped to standard concepts in the Observational Medical Outcomes Partnership common data model. A hybrid approach of combining deep learning-based models, curated lexicons, and pattern-based rules was applied to quickly build the COVID-19 SignSym from CLAMP, with optimized performance. Our extensive evaluation using 3 external sites with clinical notes of COVID-19 patients, as well as the online medical dialogues of COVID-19, shows COVID-19 Sign-Sym can achieve high performance across data sources. The workflow used for this study can be generalized to other use cases, where existing clinical natural language processing tools need to be customized for specific information needs within a short time. COVID-19 SignSym is freely accessible to the research community as a downloadable package (https://clamp.uth.edu/covid/nlp.php) and has been used by 16 healthcare organizations to support clinical research of COVID-19.

Keeping track of scientific challenges, advances and emerging directions is a fundamental part of research. However, researchers face a flood of papers that hinders discovery of important knowledge. In biomedicine, this directly impacts human lives. To address this problem, we present a novel task of extraction and search of scientific challenges and directions, to facilitate rapid knowledge discovery. We construct and release an expert-annotated corpus of texts sampled from full-length papers, labeled with novel semantic categories that generalize across many types of challenges and directions. We focus on a large corpus of interdisciplinary work relating to the COVID-19 pandemic, ranging from biomedicine to areas such as AI and economics. We apply a model trained on our data to identify challenges and directions across the corpus and build a dedicated search engine. In experiments with 19 researchers and clinicians using our system, we outperform a popular scientific search engine in assisting knowledge discovery. Finally, we show that models trained on our resource generalize to the wider biomedical domain and to AI papers, highlighting its broad utility. We make our data, model and search engine publicly available. https://challenges.apps.allenai.org/

In this article, we conduct data mining to discover the countries, universities and companies, produced or collaborated the most research on Covid-19 since the pandemic started. We present some interesting findings, but despite analysing all available records on COVID-19 from the Web of Science Core Collection, we failed to reach any significant conclusions on how the world responded to the COVID-19 pandemic. Therefore, we increased our analysis to include all available data records on pandemics and epidemics from 1900 to 2020. We discover some interesting results on countries, universities and companies, that produced collaborated most the most in research on pandemic and epidemics. Then we compared the results with the analysing on COVID-19 data records. This has created some interesting findings that are explained and graphically visualised in the article.

The pandemic resulted in vast repositories of unstructured data, including radiology reports, due to increased medical examinations. Previous research on automated diagnosis of COVID-19 primarily focuses on X-ray images, despite their lower precision compared to computed tomography (CT) scans. In this work, we leverage unstructured data from a hospital and harness the fine-grained details offered by CT scans to perform zero-shot multi-label classification based on contrastive visual language learning. In collaboration with human experts, we investigate the effectiveness of multiple zero-shot models that aid radiologists in detecting pulmonary embolisms and identifying intricate lung details like ground glass opacities and consolidations. Our empirical analysis provides an overview of the possible solutions to target such fine-grained tasks, so far overlooked in the medical multimodal pretraining literature. Our investigation promises future advancements in the medical image analysis community by addressing some challenges associated with unstructured data and fine-grained multi-label classification.

Background: Social media platforms have become a viable source of medical information, with patients and healthcare professionals using them to share health-related information and track diseases. Similarly, YouTube, the largest video-sharing platform in the world contains vlogs where individuals talk about their illnesses. The aim of our study was to investigate the use of Natural Language Processing (NLP) to identify the spoken content of YouTube vlogs related to the diagnosis of Coronavirus disease of 2019 (COVID-19) for public health screening. Methods: COVID-19 videos on YouTube were searched using relevant keywords. A total of 1000 videos being spoken in English were downloaded out of which 791 were classified as vlogs, 192 were non-vlogs, and 17 were deleted by the channel. The videos were converted into a textual format using Microsoft Streams. The textual data was preprocessed using basic and advanced preprocessing methods. A lexicon of 200 words was created which contained words related to COVID-19. The data was analyzed using topic modeling, word clouds, and lexicon matching. Results: The word cloud results revealed discussions about COVID-19 symptoms like "fever", along with generic terms such as "mask" and "isolation". Lexical analysis demonstrated that in 96.46% of videos, patients discussed generic terms, and in 95.45% of videos, people talked about COVID-19 symptoms. LDA Topic Modeling results also generated topics that successfully captured key themes and content related to our investigation of COVID-19 diagnoses in YouTube vlogs. Conclusion: By leveraging NLP techniques on YouTube vlogs public health practitioners can enhance their ability to mitigate the effects of pandemics and effectively respond to public health challenges.

The outbreak of COVID-19 has shocked the entire world with its fairly rapid spread and has challenged different sectors. One of the most effective ways to limit its spread is the early and accurate diagnosing infected patients. Medical imaging, such as X-ray and Computed Tomography (CT), combined with the potential of Artificial Intelligence (AI), plays an essential role in supporting medical personnel in the diagnosis process. Thus, in this article five different deep learning models (ResNet18, ResNet34, InceptionV3, InceptionResNetV2 and DenseNet161) and their ensemble, using majority voting have been used to classify COVID-19, pneumoni{\ae} and healthy subjects using chest X-ray images. Multilabel classification was performed to predict multiple pathologies for each patient, if present. Firstly, the interpretability of each of the networks was thoroughly studied using local interpretability methods - occlusion, saliency, input X gradient, guided backpropagation, integrated gradients, and DeepLIFT, and using a global technique - neuron activation profiles. The mean Micro-F1 score of the models for COVID-19 classifications ranges from 0.66 to 0.875, and is 0.89 for the ensemble of the network models. The qualitative results showed that the ResNets were the most interpretable models. This research demonstrates the importance of using interpretability methods to compare different models before making a decision regarding the best performing model.

Background: Health datasets from clinical sources do not reflect the breadth and diversity of disease in the real world, impacting research, medical education, and artificial intelligence (AI) tool development. Dermatology is a suitable area to develop and test a new and scalable method to create representative health datasets. Methods: We used Google Search advertisements to invite contributions to an open access dataset of images of dermatology conditions, demographic and symptom information. With informed contributor consent, we describe and release this dataset containing 10,408 images from 5,033 contributions from internet users in the United States over 8 months starting March 2023. The dataset includes dermatologist condition labels as well as estimated Fitzpatrick Skin Type (eFST) and Monk Skin Tone (eMST) labels for the images. Results: We received a median of 22 submissions/day (IQR 14-30). Female (66.72%) and younger (52% < age 40) contributors had a higher representation in the dataset compared to the US population, and 32.6% of contributors reported a non-White racial or ethnic identity. Over 97.5% of contributions were genuine images of skin conditions. Dermatologist confidence in assigning a differential diagnosis increased with the number of available variables, and showed a weaker correlation with image sharpness (Spearman's P values <0.001 and 0.01 respectively). Most contributions were short-duration (54% with onset < 7 days ago ) and 89% were allergic, infectious, or inflammatory conditions. eFST and eMST distributions reflected the geographical origin of the dataset. The dataset is available at github.com/google-research-datasets/scin . Conclusion: Search ads are effective at crowdsourcing images of health conditions. The SCIN dataset bridges important gaps in the availability of representative images of common skin conditions.

Spreading of COVID-19 virus has increased the efforts to provide testing kits. Not only the preparation of these kits had been hard, rare, and expensive but also using them is another issue. Results have shown that these kits take some crucial time to recognize the virus, in addition to the fact that they encounter with 30% loss. In this paper, we have studied the usage of x-ray pictures which are ubiquitous, for the classification of COVID-19 chest Xray images, by the existing convolutional neural networks (CNNs). We intend to train chest x-rays of infected and not infected ones with different CNNs architectures including VGG19, Densnet-121, and Xception. Training these architectures resulted in different accuracies which were much faster and more precise than usual ways of testing.

To combat COVID-19, both clinicians and scientists need to digest vast amounts of relevant biomedical knowledge in scientific literature to understand the disease mechanism and related biological functions. We have developed a novel and comprehensive knowledge discovery framework, COVID-KG to extract fine-grained multimedia knowledge elements (entities and their visual chemical structures, relations, and events) from scientific literature. We then exploit the constructed multimedia knowledge graphs (KGs) for question answering and report generation, using drug repurposing as a case study. Our framework also provides detailed contextual sentences, subfigures, and knowledge subgraphs as evidence.

Clinical trials disruption has always represented a non negligible part of the ending of interventional studies. While the SARS-CoV-2 (COVID-19) pandemic has led to an impressive and unprecedented initiation of clinical research, it has also led to considerable disruption of clinical trials in other disease areas, with around 80% of non-COVID-19 trials stopped or interrupted during the pandemic. In many cases the disrupted trials will not have the planned statistical power necessary to yield interpretable results. This paper describes methods to compensate for the information loss arising from trial disruptions by incorporating additional information available from auxiliary data sources. The methods described include the use of auxiliary data on baseline and early outcome data available from the trial itself and frequentist and Bayesian approaches for the incorporation of information from external data sources. The methods are illustrated by application to the analysis of artificial data based on the Primary care pediatrics Learning Activity Nutrition (PLAN) study, a clinical trial assessing a diet and exercise intervention for overweight children, that was affected by the COVID-19 pandemic. We show how all of the methods proposed lead to an increase in precision relative to use of complete case data only.

People increasingly search online for answers to their medical questions but the rate at which medical questions are asked online significantly exceeds the capacity of qualified people to answer them. This leaves many questions unanswered or inadequately answered. Many of these questions are not unique, and reliable identification of similar questions would enable more efficient and effective question answering schema. COVID-19 has only exacerbated this problem. Almost every government agency and healthcare organization has tried to meet the informational need of users by building online FAQs, but there is no way for people to ask their question and know if it is answered on one of these pages. While many research efforts have focused on the problem of general question similarity, these approaches do not generalize well to domains that require expert knowledge to determine semantic similarity, such as the medical domain. In this paper, we show how a double fine-tuning approach of pretraining a neural network on medical question-answer pairs followed by fine-tuning on medical question-question pairs is a particularly useful intermediate task for the ultimate goal of determining medical question similarity. While other pretraining tasks yield an accuracy below 78.7% on this task, our model achieves an accuracy of 82.6% with the same number of training examples, an accuracy of 80.0% with a much smaller training set, and an accuracy of 84.5% when the full corpus of medical question-answer data is used. We also describe a currently live system that uses the trained model to match user questions to COVID-related FAQs.

The COVID-19 pandemic is the worst pandemic to strike the world in over a century. Crucial to stemming the tide of the SARS-CoV-2 virus is communicating to vulnerable populations the means by which they can protect themselves. To this end, the collaborators forming the Translation Initiative for COvid-19 (TICO-19) have made test and development data available to AI and MT researchers in 35 different languages in order to foster the development of tools and resources for improving access to information about COVID-19 in these languages. In addition to 9 high-resourced, "pivot" languages, the team is targeting 26 lesser resourced languages, in particular languages of Africa, South Asia and South-East Asia, whose populations may be the most vulnerable to the spread of the virus. The same data is translated into all of the languages represented, meaning that testing or development can be done for any pairing of languages in the set. Further, the team is converting the test and development data into translation memories (TMXs) that can be used by localizers from and to any of the languages.

Since COVID strongly affects the respiratory system, lung CT-scans can be used for the analysis of a patients health. We introduce a neural network for the prediction of the severity of lung damage and the detection of a COVID-infection using three-dimensional CT-data. Therefore, we adapt the recent ConvNeXt model to process three-dimensional data. Furthermore, we design and analyze different pretraining methods specifically designed to improve the models ability to handle three-dimensional CT-data. We rank 2nd in the 1st COVID19 Severity Detection Challenge and 3rd in the 2nd COVID19 Detection Challenge.

The coronavirus disease (COVID-19) has resulted in a pandemic crippling the a breadth of services critical to daily life. Segmentation of lung infections in computerized tomography (CT) slices could be be used to improve diagnosis and understanding of COVID-19 in patients. Deep learning systems lack interpretability because of their black box nature. Inspired by human communication of complex ideas through language, we propose a symbolic framework based on emergent languages for the segmentation of COVID-19 infections in CT scans of lungs. We model the cooperation between two artificial agents - a Sender and a Receiver. These agents synergistically cooperate using emergent symbolic language to solve the task of semantic segmentation. Our game theoretic approach is to model the cooperation between agents unlike Generative Adversarial Networks (GANs). The Sender retrieves information from one of the higher layers of the deep network and generates a symbolic sentence sampled from a categorical distribution of vocabularies. The Receiver ingests the stream of symbols and cogenerates the segmentation mask. A private emergent language is developed that forms the communication channel used to describe the task of segmentation of COVID infections. We augment existing state of the art semantic segmentation architectures with our symbolic generator to form symbolic segmentation models. Our symbolic segmentation framework achieves state of the art performance for segmentation of lung infections caused by COVID-19. Our results show direct interpretation of symbolic sentences to discriminate between normal and infected regions, infection morphology and image characteristics. We show state of the art results for segmentation of COVID-19 lung infections in CT.

Since the COVID-19 pandemic, clinicians have seen a large and sustained influx in patient portal messages, significantly contributing to clinician burnout. To the best of our knowledge, there are no large-scale public patient portal messages corpora researchers can use to build tools to optimize clinician portal workflows. Informed by our ongoing work with a regional hospital, this study introduces an LLM-powered framework for configurable and realistic patient portal message generation. Our approach leverages few-shot grounded text generation, requiring only a small number of de-identified patient portal messages to help LLMs better match the true style and tone of real data. Clinical experts in our team deem this framework as HIPAA-friendly, unlike existing privacy-preserving approaches to synthetic text generation which cannot guarantee all sensitive attributes will be protected. Through extensive quantitative and human evaluation, we show that our framework produces data of higher quality than comparable generation methods as well as all related datasets. We believe this work provides a path forward for (i) the release of large-scale synthetic patient message datasets that are stylistically similar to ground-truth samples and (ii) HIPAA-friendly data generation which requires minimal human de-identification efforts.

This paper describes our submission on the COVID-19 literature annotation task at Biocreative VII. We proposed an approach that exploits the knowledge of the globally non-optimal weights, usually rejected, to build a rich representation of each label. Our proposed approach consists of two stages: (1) A bagging of various initializations of the training data that features weakly trained weights, (2) A stacking of heterogeneous vocabulary models based on BERT and RoBERTa Embeddings. The aggregation of these weak insights performs better than a classical globally efficient model. The purpose is the distillation of the richness of knowledge to a simpler and lighter model. Our system obtains an Instance-based F1 of 92.96 and a Label-based micro-F1 of 91.35.

Coronavirus disease 2019 (Covid-19) is highly contagious with limited treatment options. Early and accurate diagnosis of Covid-19 is crucial in reducing the spread of the disease and its accompanied mortality. Currently, detection by reverse transcriptase polymerase chain reaction (RT-PCR) is the gold standard of outpatient and inpatient detection of Covid-19. RT-PCR is a rapid method, however, its accuracy in detection is only ~70-75%. Another approved strategy is computed tomography (CT) imaging. CT imaging has a much higher sensitivity of ~80-98%, but similar accuracy of 70%. To enhance the accuracy of CT imaging detection, we developed an open-source set of algorithms called CovidCTNet that successfully differentiates Covid-19 from community-acquired pneumonia (CAP) and other lung diseases. CovidCTNet increases the accuracy of CT imaging detection to 90% compared to radiologists (70%). The model is designed to work with heterogeneous and small sample sizes independent of the CT imaging hardware. In order to facilitate the detection of Covid-19 globally and assist radiologists and physicians in the screening process, we are releasing all algorithms and parametric details in an open-source format. Open-source sharing of our CovidCTNet enables developers to rapidly improve and optimize services, while preserving user privacy and data ownership.

The coronavirus (COVID-19) pandemic has significantly altered our lifestyles as we resort to minimize the spread through preventive measures such as social distancing and quarantine. An increasingly worrying aspect is the gap between the exponential disease spread and the delay in adopting preventive measures. This gap is attributed to the lack of awareness about the disease and its preventive measures. Nowadays, social media platforms (ie., Twitter) are frequently used to create awareness about major events, including COVID-19. In this paper, we use Twitter to characterize public awareness regarding COVID-19 by analyzing the information flow in the most affected countries. Towards that, we collect more than 46K trends and 622 Million tweets from the top twenty most affected countries to examine 1) the temporal evolution of COVID-19 related trends, 2) the volume of tweets and recurring topics in those trends, and 3) the user sentiment towards preventive measures. Our results show that countries with a lower pandemic spread generated a higher volume of trends and tweets to expedite the information flow and contribute to public awareness. We also observed that in those countries, the COVID-19 related trends were generated before the sharp increase in the number of cases, indicating a preemptive attempt to notify users about the potential threat. Finally, we noticed that in countries with a lower spread, users had a positive sentiment towards COVID-19 preventive measures. Our measurements and analysis show that effective social media usage can influence public behavior, which can be leveraged to better combat future pandemics.

Medical research generates a large number of publications with the PubMed database already containing >35 million research articles. Integration of the knowledge scattered across this large body of literature could provide key insights into physiological mechanisms and disease processes leading to novel medical interventions. However, it is a great challenge for researchers to utilize this information in full since the scale and complexity of the data greatly surpasses human processing abilities. This becomes especially problematic in cases of extreme urgency like the COVID-19 pandemic. Automated text mining can help extract and connect information from the large body of medical research articles. The first step in text mining is typically the identification of specific classes of keywords (e.g., all protein or disease names), so called Named Entity Recognition (NER). Here we present an end-to-end pipeline for NER of typical entities found in medical research articles, including diseases, cells, chemicals, genes/proteins, and species. The pipeline can access and process large medical research article collections (PubMed, CORD-19) or raw text and incorporates a series of deep learning models fine-tuned on the HUNER corpora collection. In addition, the pipeline can perform dictionary-based NER related to COVID-19 and other medical topics. Users can also load their own NER models and dictionaries to include additional entities. The output consists of publication-ready ranked lists and graphs of detected entities and files containing the annotated texts. An associated script allows rapid inspection of the results for specific entities of interest. As model use cases, the pipeline was deployed on two collections of autophagy-related abstracts from PubMed and on the CORD19 dataset, a collection of 764 398 research article abstracts related to COVID-19.

Recent research in disaster informatics demonstrates a practical and important use case of artificial intelligence to save human lives and suffering during natural disasters based on social media contents (text and images). While notable progress has been made using texts, research on exploiting the images remains relatively under-explored. To advance image-based approaches, we propose MEDIC (Available at: https://crisisnlp.qcri.org/medic/index.html), which is the largest social media image classification dataset for humanitarian response consisting of 71,198 images to address four different tasks in a multi-task learning setup. This is the first dataset of its kind: social media images, disaster response, and multi-task learning research. An important property of this dataset is its high potential to facilitate research on multi-task learning, which recently receives much interest from the machine learning community and has shown remarkable results in terms of memory, inference speed, performance, and generalization capability. Therefore, the proposed dataset is an important resource for advancing image-based disaster management and multi-task machine learning research. We experiment with different deep learning architectures and report promising results, which are above the majority baselines for all tasks. Along with the dataset, we also release all relevant scripts (https://github.com/firojalam/medic).

With the advent of the COVID-19 pandemic, ultrasound imaging has emerged as a promising technique for COVID-19 detection, due to its non-invasive nature, affordability, and portability. In response, researchers have focused on developing AI-based scoring systems to provide real-time diagnostic support. However, the limited size and lack of proper annotation in publicly available ultrasound datasets pose significant challenges for training a robust AI model. This paper proposes MeDiVLAD, a novel pipeline to address the above issue for multi-level lung-ultrasound (LUS) severity scoring. In particular, we leverage self-knowledge distillation to pretrain a vision transformer (ViT) without label and aggregate frame-level features via dual-level VLAD aggregation. We show that with minimal finetuning, MeDiVLAD outperforms conventional fully-supervised methods in both frame- and video-level scoring, while offering classification reasoning with exceptional quality. This superior performance enables key applications such as the automatic identification of critical lung pathology areas and provides a robust solution for broader medical video classification tasks.

The COVID-19 pandemic has accentuated socioeconomic disparities across various racial and ethnic groups in the United States. While previous studies have utilized traditional survey methods like the Household Pulse Survey (HPS) to elucidate these disparities, this paper explores the role of social media platforms in both highlighting and addressing these challenges. Drawing from real-time data sourced from Twitter, we analyzed language patterns related to four major types of adverse experiences: loss of employment income (LI), food scarcity (FS), housing insecurity (HI), and unmet needs for mental health services (UM). We first formulate a sparsity optimization problem that extracts low-level language features from social media data sources. Second, we propose novel constraints on feature similarity exploiting prior knowledge about the similarity of the language patterns among the adverse experiences. The proposed problem is challenging to solve due to the non-convexity objective and non-smoothness penalties. We develop an algorithm based on the alternating direction method of multipliers (ADMM) framework to solve the proposed formulation. Extensive experiments and comparisons to other models on real-world social media and the detection of adverse experiences justify the efficacy of our model.

The cycle of scientific discovery is frequently bottlenecked by the slow, manual creation of software to support computational experiments. To address this, we present an AI system that creates expert-level scientific software whose goal is to maximize a quality metric. The system uses a Large Language Model (LLM) and Tree Search (TS) to systematically improve the quality metric and intelligently navigate the large space of possible solutions. The system achieves expert-level results when it explores and integrates complex research ideas from external sources. The effectiveness of tree search is demonstrated across a wide range of benchmarks. In bioinformatics, it discovered 40 novel methods for single-cell data analysis that outperformed the top human-developed methods on a public leaderboard. In epidemiology, it generated 14 models that outperformed the CDC ensemble and all other individual models for forecasting COVID-19 hospitalizations. Our method also produced state-of-the-art software for geospatial analysis, neural activity prediction in zebrafish, time series forecasting and numerical solution of integrals. By devising and implementing novel solutions to diverse tasks, the system represents a significant step towards accelerating scientific progress.

The face is a rich source of information that can be utilized to infer a person's biological age, sex, phenotype, genetic defects, and health status. All of these factors are relevant for predicting an individual's remaining lifespan. In this study, we collected a dataset of over 24,000 images (from Wikidata/Wikipedia) of individuals who died of natural causes, along with the number of years between when the image was taken and when the person passed away. We made this dataset publicly available. We fine-tuned multiple Convolutional Neural Network (CNN) models on this data, at best achieving a mean absolute error of 8.3 years in the validation data using VGGFace. However, the model's performance diminishes when the person was younger at the time of the image. To demonstrate the potential applications of our remaining lifespan model, we present examples of using it to estimate the average loss of life (in years) due to the COVID-19 pandemic and to predict the increase in life expectancy that might result from a health intervention such as weight loss. Additionally, we discuss the ethical considerations associated with such models.

In this paper we discuss an in-progress work on the development of a speech corpus for four low-resource Indo-Aryan languages -- Awadhi, Bhojpuri, Braj and Magahi using the field methods of linguistic data collection. The total size of the corpus currently stands at approximately 18 hours (approx. 4-5 hours each language) and it is transcribed and annotated with grammatical information such as part-of-speech tags, morphological features and Universal dependency relationships. We discuss our methodology for data collection in these languages, most of which was done in the middle of the COVID-19 pandemic, with one of the aims being to generate some additional income for low-income groups speaking these languages. In the paper, we also discuss the results of the baseline experiments for automatic speech recognition system in these languages.

The work of this paper presents a dataset that contains the data of 4011 videos about the ongoing outbreak of measles published on 264 websites on the internet between January 1, 2024, and May 31, 2024. The dataset is available at https://dx.doi.org/10.21227/40s8-xf63. These websites primarily include YouTube and TikTok, which account for 48.6% and 15.2% of the videos, respectively. The remainder of the websites include Instagram and Facebook as well as the websites of various global and local news organizations. For each of these videos, the URL of the video, title of the post, description of the post, and the date of publication of the video are presented as separate attributes in the dataset. After developing this dataset, sentiment analysis (using VADER), subjectivity analysis (using TextBlob), and fine-grain sentiment analysis (using DistilRoBERTa-base) of the video titles and video descriptions were performed. This included classifying each video title and video description into (i) one of the sentiment classes i.e. positive, negative, or neutral, (ii) one of the subjectivity classes i.e. highly opinionated, neutral opinionated, or least opinionated, and (iii) one of the fine-grain sentiment classes i.e. fear, surprise, joy, sadness, anger, disgust, or neutral. These results are presented as separate attributes in the dataset for the training and testing of machine learning algorithms for performing sentiment analysis or subjectivity analysis in this field as well as for other applications. Finally, this paper also presents a list of open research questions that may be investigated using this dataset.

Skin lesion datasets provide essential information for understanding various skin conditions and developing effective diagnostic tools. They aid the artificial intelligence-based early detection of skin cancer, facilitate treatment planning, and contribute to medical education and research. Published large datasets have partially coverage the subclassifications of the skin lesions. This limitation highlights the need for more expansive and varied datasets to reduce false predictions and help improve the failure analysis for skin lesions. This study presents a diverse dataset comprising 12,345 dermatoscopic images with 38 subclasses of skin lesions collected in Turkiye which comprises different skin types in the transition zone between Europe and Asia. Each subgroup contains high-resolution photos and expert annotations, providing a strong and reliable basis for future research. The detailed analysis of each subgroup provided in this study facilitates targeted research endeavors and enhances the depth of understanding regarding the skin lesions. This dataset distinguishes itself through a diverse structure with 5 super classes, 15 main classes, 38 subclasses and its 12,345 high-resolution dermatoscopic images.

After being collected for patient care, Observational Health Data (OHD) can further benefit patient well-being by sustaining the development of health informatics and medical research. Vast potential is unexploited because of the fiercely private nature of patient-related data and regulations to protect it. Generative Adversarial Networks (GANs) have recently emerged as a groundbreaking way to learn generative models that produce realistic synthetic data. They have revolutionized practices in multiple domains such as self-driving cars, fraud detection, digital twin simulations in industrial sectors, and medical imaging. The digital twin concept could readily apply to modelling and quantifying disease progression. In addition, GANs posses many capabilities relevant to common problems in healthcare: lack of data, class imbalance, rare diseases, and preserving privacy. Unlocking open access to privacy-preserving OHD could be transformative for scientific research. In the midst of COVID-19, the healthcare system is facing unprecedented challenges, many of which of are data related for the reasons stated above. Considering these facts, publications concerning GAN applied to OHD seemed to be severely lacking. To uncover the reasons for this slow adoption, we broadly reviewed the published literature on the subject. Our findings show that the properties of OHD were initially challenging for the existing GAN algorithms (unlike medical imaging, for which state-of-the-art model were directly transferable) and the evaluation synthetic data lacked clear metrics. We find more publications on the subject than expected, starting slowly in 2017, and since then at an increasing rate. The difficulties of OHD remain, and we discuss issues relating to evaluation, consistency, benchmarking, data modelling, and reproducibility.

A comprehensive bibliographic review with R statistical methods of the COVID pandemic in PubMed literature and Web of Science Core Collection, supported with Google Scholar search. In addition, a case study review of emerging new approaches in different regions, using medical literature, academic literature, news articles and other reliable data sources. Public responses of mistrust about privacy data misuse differ across countries, depending on the chosen public communication strategy.

The rapid evolution of artificial intelligence (AI), together with the increased availability of social media and news for epidemiological surveillance, are marking a pivotal moment in epidemiology and public health research. Leveraging the power of generative AI, we use an ensemble approach which incorporates multiple Large Language Models (LLMs) to extract valuable actionable epidemiological information from the World Health Organization (WHO) Disease Outbreak News (DONs). DONs is a collection of regular reports on global outbreaks curated by the WHO and the adopted decision-making processes to respond to them. The extracted information is made available in a daily-updated dataset and a knowledge graph, referred to as eKG, derived to provide a nuanced representation of the public health domain knowledge. We provide an overview of this new dataset and describe the structure of eKG, along with the services and tools used to access and utilize the data that we are building on top. These innovative data resources open altogether new opportunities for epidemiological research, and the analysis and surveillance of disease outbreaks.

Timely and effective response to humanitarian crises requires quick and accurate analysis of large amounts of text data - a process that can highly benefit from expert-assisted NLP systems trained on validated and annotated data in the humanitarian response domain. To enable creation of such NLP systems, we introduce and release HumSet, a novel and rich multilingual dataset of humanitarian response documents annotated by experts in the humanitarian response community. The dataset provides documents in three languages (English, French, Spanish) and covers a variety of humanitarian crises from 2018 to 2021 across the globe. For each document, HUMSET provides selected snippets (entries) as well as assigned classes to each entry annotated using common humanitarian information analysis frameworks. HUMSET also provides novel and challenging entry extraction and multi-label entry classification tasks. In this paper, we take a first step towards approaching these tasks and conduct a set of experiments on Pre-trained Language Models (PLM) to establish strong baselines for future research in this domain. The dataset is available at https://blog.thedeep.io/humset/.

This paper introduces the Pandemic PACT Advanced Categorisation Engine (PPACE) along with its associated dataset. PPACE is a fine-tuned model developed to automatically classify research abstracts from funded biomedical projects according to WHO-aligned research priorities. This task is crucial for monitoring research trends and identifying gaps in global health preparedness and response. Our approach builds on human-annotated projects, which are allocated one or more categories from a predefined list. A large language model is then used to generate `rationales' explaining the reasoning behind these annotations. This augmented data, comprising expert annotations and rationales, is subsequently used to fine-tune a smaller, more efficient model. Developed as part of the Pandemic PACT project, which aims to track and analyse research funding and clinical evidence for a wide range of diseases with outbreak potential, PPACE supports informed decision-making by research funders, policymakers, and independent researchers. We introduce and release both the trained model and the instruction-based dataset used for its training. Our evaluation shows that PPACE significantly outperforms its baselines. The release of PPACE and its associated dataset offers valuable resources for researchers in multilabel biomedical document classification and supports advancements in aligning biomedical research with key global health priorities.

Accurately forecasting patient arrivals at Urgent Care Clinics (UCCs) and Emergency Departments (EDs) is important for effective resourcing and patient care. However, correctly estimating patient flows is not straightforward since it depends on many drivers. The predictability of patient arrivals has recently been further complicated by the COVID-19 pandemic conditions and the resulting lockdowns. This study investigates how a suite of novel quasi-real-time variables like Google search terms, pedestrian traffic, the prevailing incidence levels of influenza, as well as the COVID-19 Alert Level indicators can both generally improve the forecasting models of patient flows and effectively adapt the models to the unfolding disruptions of pandemic conditions. This research also uniquely contributes to the body of work in this domain by employing tools from the eXplainable AI field to investigate more deeply the internal mechanics of the models than has previously been done. The Voting ensemble-based method combining machine learning and statistical techniques was the most reliable in our experiments. Our study showed that the prevailing COVID-19 Alert Level feature together with Google search terms and pedestrian traffic were effective at producing generalisable forecasts. The implications of this study are that proxy variables can effectively augment standard autoregressive features to ensure accurate forecasting of patient flows. The experiments showed that the proposed features are potentially effective model inputs for preserving forecast accuracies in the event of future pandemic outbreaks.

The demand for emergency department (ED) services is increasing across the globe, particularly during the current COVID-19 pandemic. Clinical triage and risk assessment have become increasingly challenging due to the shortage of medical resources and the strain on hospital infrastructure caused by the pandemic. As a result of the widespread use of electronic health records (EHRs), we now have access to a vast amount of clinical data, which allows us to develop predictive models and decision support systems to address these challenges. To date, however, there are no widely accepted benchmark ED triage prediction models based on large-scale public EHR data. An open-source benchmarking platform would streamline research workflows by eliminating cumbersome data preprocessing, and facilitate comparisons among different studies and methodologies. In this paper, based on the Medical Information Mart for Intensive Care IV Emergency Department (MIMIC-IV-ED) database, we developed a publicly available benchmark suite for ED triage predictive models and created a benchmark dataset that contains over 400,000 ED visits from 2011 to 2019. We introduced three ED-based outcomes (hospitalization, critical outcomes, and 72-hour ED reattendance) and implemented a variety of popular methodologies, ranging from machine learning methods to clinical scoring systems. We evaluated and compared the performance of these methods against benchmark tasks. Our codes are open-source, allowing anyone with MIMIC-IV-ED data access to perform the same steps in data processing, benchmark model building, and experiments. This study provides future researchers with insights, suggestions, and protocols for managing raw data and developing risk triaging tools for emergency care.

Urgent care clinics and emergency departments around the world periodically suffer from extended wait times beyond patient expectations due to inadequate staffing levels. These delays have been linked with adverse clinical outcomes. Previous research into forecasting demand this domain has mostly used a collection of statistical techniques, with machine learning approaches only now beginning to emerge in recent literature. The forecasting problem for this domain is difficult and has also been complicated by the COVID-19 pandemic which has introduced an additional complexity to this estimation due to typical demand patterns being disrupted. This study explores the ability of machine learning methods to generate accurate patient presentations at two large urgent care clinics located in Auckland, New Zealand. A number of machine learning algorithms were explored in order to determine the most effective technique for this problem domain, with the task of making forecasts of daily patient demand three months in advance. The study also performed an in-depth analysis into the model behaviour in respect to the exploration of which features are most effective at predicting demand and which features are capable of adaptation to the volatility caused by the COVID-19 pandemic lockdowns. The results showed that ensemble-based methods delivered the most accurate and consistent solutions on average, generating improvements in the range of 23%-27% over the existing in-house methods for estimating the daily demand.

The COVID-19 pandemic has escalated mental health crises worldwide, with social isolation and economic instability contributing to a rise in suicidal behavior. Suicide can result from social factors such as shame, abuse, abandonment, and mental health conditions like depression, Post-Traumatic Stress Disorder (PTSD), Attention-Deficit/Hyperactivity Disorder (ADHD), anxiety disorders, and bipolar disorders. As these conditions develop, signs of suicidal ideation may manifest in social media interactions. Analyzing social media data using artificial intelligence (AI) techniques can help identify patterns of suicidal behavior, providing invaluable insights for suicide prevention agencies, professionals, and broader community awareness initiatives. Machine learning algorithms for this purpose require large volumes of accurately labeled data. Previous research has not fully explored the potential of incorporating explanations in analyzing and labeling longitudinal social media data. In this study, we employed a model explanation method, Layer Integrated Gradients, on top of a fine-tuned state-of-the-art language model, to assign each token from Reddit users' posts an attribution score for predicting suicidal ideation. By extracting and analyzing attributions of tokens from the data, we propose a methodology for preliminary screening of social media posts for suicidal ideation without using large language models during inference.

We present CoNTACT: a Dutch language model adapted to the domain of COVID-19 tweets. The model was developed by continuing the pre-training phase of RobBERT (Delobelle, 2020) by using 2.8M Dutch COVID-19 related tweets posted in 2021. In order to test the performance of the model and compare it to RobBERT, the two models were tested on two tasks: (1) binary vaccine hesitancy detection and (2) detection of arguments for vaccine hesitancy. For both tasks, not only Twitter but also Facebook data was used to show cross-genre performance. In our experiments, CoNTACT showed statistically significant gains over RobBERT in all experiments for task 1. For task 2, we observed substantial improvements in virtually all classes in all experiments. An error analysis indicated that the domain adaptation yielded better representations of domain-specific terminology, causing CoNTACT to make more accurate classification decisions.

Building AI models with trustworthiness is important especially in regulated areas such as healthcare. In tackling COVID-19, previous work uses convolutional neural networks as the backbone architecture, which has shown to be prone to over-caution and overconfidence in making decisions, rendering them less trustworthy -- a crucial flaw in the context of medical imaging. In this study, we propose a feature learning approach using Vision Transformers, which use an attention-based mechanism, and examine the representation learning capability of Transformers as a new backbone architecture for medical imaging. Through the task of classifying COVID-19 chest radiographs, we investigate into whether generalization capabilities benefit solely from Vision Transformers' architectural advances. Quantitative and qualitative evaluations are conducted on the trustworthiness of the models, through the use of "trust score" computation and a visual explainability technique. We conclude that the attention-based feature learning approach is promising in building trustworthy deep learning models for healthcare.

Natural disasters, such as floods, tornadoes, or wildfires, are increasingly pervasive as the Earth undergoes global warming. It is difficult to predict when and where an incident will occur, so timely emergency response is critical to saving the lives of those endangered by destructive events. Fortunately, technology can play a role in these situations. Social media posts can be used as a low-latency data source to understand the progression and aftermath of a disaster, yet parsing this data is tedious without automated methods. Prior work has mostly focused on text-based filtering, yet image and video-based filtering remains largely unexplored. In this work, we present the Incidents1M Dataset, a large-scale multi-label dataset which contains 977,088 images, with 43 incident and 49 place categories. We provide details of the dataset construction, statistics and potential biases; introduce and train a model for incident detection; and perform image-filtering experiments on millions of images on Flickr and Twitter. We also present some applications on incident analysis to encourage and enable future work in computer vision for humanitarian aid. Code, data, and models are available at http://incidentsdataset.csail.mit.edu.

Seeking health-related advice on the internet has become a common practice in the digital era. Determining the trustworthiness of medical claims found online and finding appropriate evidence for this information is increasingly challenging. Fact-checking has emerged as an approach to assess the veracity of factual claims using evidence from credible knowledge sources. To help advance the automation of this task, in this paper, we introduce a novel dataset of 750 health-related claims, labeled for veracity by medical experts and backed with evidence from appropriate clinical studies. We provide an analysis of the dataset, highlighting its characteristics and challenges. The dataset can be used for Machine Learning tasks related to automated fact-checking such as evidence retrieval, veracity prediction, and explanation generation. For this purpose, we provide baseline models based on different approaches, examine their performance, and discuss the findings.

Objective digital data is scarce yet needed in many domains to enable research that can transform the standard of healthcare. While data from consumer-grade wearables and smartphones is more accessible, there is critical need for similar data from clinical-grade devices used by patients with a diagnosed condition. The prevalence of wearable medical devices in the diabetes domain sets the stage for unique research and development within this field and beyond. However, the scarcity of open-source datasets presents a major barrier to progress. To facilitate broader research on diabetes-relevant problems and accelerate development of robust computational solutions, we provide the DiaTrend dataset. The DiaTrend dataset is composed of intensive longitudinal data from wearable medical devices, including a total of 27,561 days of continuous glucose monitor data and 8,220 days of insulin pump data from 54 patients with diabetes. This dataset is useful for developing novel analytic solutions that can reduce the disease burden for people living with diabetes and increase knowledge on chronic condition management in outpatient settings.

This paper introduces the Emirates Multi-Task (EMT) dataset - the first publicly available dataset for autonomous driving collected in the Arab Gulf region. The EMT dataset captures the unique road topology, high traffic congestion, and distinctive characteristics of the Gulf region, including variations in pedestrian clothing and weather conditions. It contains over 30,000 frames from a dash-camera perspective, along with 570,000 annotated bounding boxes, covering approximately 150 kilometers of driving routes. The EMT dataset supports three primary tasks: tracking, trajectory forecasting and intention prediction. Each benchmark dataset is complemented with corresponding evaluations: (1) multi-agent tracking experiments, focusing on multi-class scenarios and occlusion handling; (2) trajectory forecasting evaluation using deep sequential and interaction-aware models; and (3) intention benchmark experiments conducted for predicting agents intentions from observed trajectories. The dataset is publicly available at avlab.io/emt-dataset, and pre-processing scripts along with evaluation models can be accessed at github.com/AV-Lab/emt-dataset.

This work introduces a dataset focused on fake news in US political speeches, specifically examining racial slurs and biases. By scraping and annotating 40,000 news articles, using advanced NLP tools and human verification, we provide a nuanced understanding of misinformation in political discourse. The dataset, designed for machine learning and bias analysis, is a critical resource for researchers, policymakers, and educators. It facilitates the development of strategies against misinformation and enhances media literacy, marking a significant contribution to the study of fake news and political communication. Our dataset, focusing on the analysis of fake news in the context of the 2024 elections, is publicly accessible for community to work on fake news identification. Our dataset, focusing on the analysis of fake news in the context of the 2024 elections, is publicly accessible.

In this paper, we explore the use of large language models to assess human interpretations of real world events. To do so, we use a language model trained prior to 2020 to artificially generate news articles concerning COVID-19 given the headlines of actual articles written during the pandemic. We then compare stylistic qualities of our artificially generated corpus with a news corpus, in this case 5,082 articles produced by CBC News between January 23 and May 5, 2020. We find our artificially generated articles exhibits a considerably more negative attitude towards COVID and a significantly lower reliance on geopolitical framing. Our methods and results hold importance for researchers seeking to simulate large scale cultural processes via recent breakthroughs in text generation.

We present a labeled large-scale, high resolution chest x-ray dataset for the automated exploration of medical images along with their associated reports. This dataset includes more than 160,000 images obtained from 67,000 patients that were interpreted and reported by radiologists at Hospital San Juan Hospital (Spain) from 2009 to 2017, covering six different position views and additional information on image acquisition and patient demography. The reports were labeled with 174 different radiographic findings, 19 differential diagnoses and 104 anatomic locations organized as a hierarchical taxonomy and mapped onto standard Unified Medical Language System (UMLS) terminology. Of these reports, 27% were manually annotated by trained physicians and the remaining set was labeled using a supervised method based on a recurrent neural network with attention mechanisms. The labels generated were then validated in an independent test set achieving a 0.93 Micro-F1 score. To the best of our knowledge, this is one of the largest public chest x-ray database suitable for training supervised models concerning radiographs, and the first to contain radiographic reports in Spanish. The PadChest dataset can be downloaded from http://bimcv.cipf.es/bimcv-projects/padchest/.

The digitization of medical records ushered in a new era of big data to clinical science, and with it the possibility that data could be shared, to multiply insights beyond what investigators could abstract from paper records. The need to share individual-level medical data to accelerate innovation in precision medicine continues to grow, and has never been more urgent, as scientists grapple with the COVID-19 pandemic. However, enthusiasm for the use of big data has been tempered by a fully appropriate concern for patient autonomy and privacy. That is, the ability to extract private or confidential information about an individual, in practice, renders it difficult to share data, since significant infrastructure and data governance must be established before data can be shared. Although HIPAA provided de-identification as an approved mechanism for data sharing, linkage attacks were identified as a major vulnerability. A variety of mechanisms have been established to avoid leaking private information, such as field suppression or abstraction, strictly limiting the amount of information that can be shared, or employing mathematical techniques such as differential privacy. Another approach, which we focus on here, is creating synthetic data that mimics the underlying data. For synthetic data to be a useful mechanism in support of medical innovation and a proxy for real-world evidence, one must demonstrate two properties of the synthetic dataset: (1) any analysis on the real data must be matched by analysis of the synthetic data (statistical fidelity) and (2) the synthetic data must preserve privacy, with minimal risk of re-identification (privacy guarantee). In this paper we propose a framework for quantifying the statistical fidelity and privacy preservation properties of synthetic datasets and demonstrate these metrics for synthetic data generated by Syntegra technology.

Background: Cancer remains one of the leading causes of morbidity and mortality worldwide. Comprehensive datasets that combine histopathological images with genetic and survival data across various tumour sites are essential for advancing computational pathology and personalised medicine. Results: We present SurGen, a dataset comprising 1,020 H&E-stained whole slide images (WSIs) from 843 colorectal cancer cases. The dataset includes detailed annotations for key genetic mutations (KRAS, NRAS, BRAF) and mismatch repair status, as well as survival data for 426 cases. To demonstrate SurGen's practical utility, we conducted a proof-of-concept machine learning experiment predicting mismatch repair status from the WSIs, achieving a test AUROC of 0.8316. These preliminary results underscore the dataset's potential to facilitate research in biomarker discovery, prognostic modelling, and advanced machine learning applications in colorectal cancer. Conclusions: SurGen offers a valuable resource for the scientific community, enabling studies that require high-quality WSIs linked with comprehensive clinical and genetic information on colorectal cancer. Our initial findings affirm the dataset's capacity to advance diagnostic precision and foster the development of personalised treatment strategies in colorectal oncology. Data available online at https://doi.org/10.6019/S-BIAD1285.

In this paper, we introduce a dataset of multilingual news articles covering the 2021 Tokyo Olympics. A total of 10,940 news articles were gathered from 1,918 different publishers, covering 1,350 sub-events of the 2021 Olympics, and published between July 1, 2021, and August 14, 2021. These articles are written in nine languages from different language families and in different scripts. To create the dataset, the raw news articles were first retrieved via a service that collects and analyzes news articles. Then, the articles were grouped using an online clustering algorithm, with each group containing articles reporting on the same sub-event. Finally, the groups were manually annotated and evaluated. The development of this dataset aims to provide a resource for evaluating the performance of multilingual news clustering algorithms, for which limited datasets are available. It can also be used to analyze the dynamics and events of the 2021 Tokyo Olympics from different perspectives. The dataset is available in CSV format and can be accessed from the CLARIN.SI repository.

Foodborne illness is a serious but preventable public health problem -- with delays in detecting the associated outbreaks resulting in productivity loss, expensive recalls, public safety hazards, and even loss of life. While social media is a promising source for identifying unreported foodborne illnesses, there is a dearth of labeled datasets for developing effective outbreak detection models. To accelerate the development of machine learning-based models for foodborne outbreak detection, we thus present TWEET-FID (TWEET-Foodborne Illness Detection), the first publicly available annotated dataset for multiple foodborne illness incident detection tasks. TWEET-FID collected from Twitter is annotated with three facets: tweet class, entity type, and slot type, with labels produced by experts as well as by crowdsource workers. We introduce several domain tasks leveraging these three facets: text relevance classification (TRC), entity mention detection (EMD), and slot filling (SF). We describe the end-to-end methodology for dataset design, creation, and labeling for supporting model development for these tasks. A comprehensive set of results for these tasks leveraging state-of-the-art single- and multi-task deep learning methods on the TWEET-FID dataset are provided. This dataset opens opportunities for future research in foodborne outbreak detection.

During the COVID-19 pandemic, a significant effort has gone into developing ML-driven epidemic forecasting techniques. However, benchmarks do not exist to claim if a new AI/ML technique is better than the existing ones. The "covid-forecast-hub" is a collection of more than 30 teams, including us, that submit their forecasts weekly to the CDC. It is not possible to declare whether one method is better than the other using those forecasts because each team's submission may correspond to different techniques over the period and involve human interventions as the teams are continuously changing/tuning their approach. Such forecasts may be considered "human-expert" forecasts and do not qualify as AI/ML approaches, although they can be used as an indicator of human expert performance. We are interested in supporting AI/ML research in epidemic forecasting which can lead to scalable forecasting without human intervention. Which modeling technique, learning strategy, and data pre-processing technique work well for epidemic forecasting is still an open problem. To help advance the state-of-the-art AI/ML applied to epidemiology, a benchmark with a collection of performance points is needed and the current "state-of-the-art" techniques need to be identified. We propose EpiBench a platform consisting of community-driven benchmarks for AI/ML applied to epidemic forecasting to standardize the challenge with a uniform evaluation protocol. In this paper, we introduce a prototype of EpiBench which is currently running and accepting submissions for the task of forecasting COVID-19 cases and deaths in the US states and We demonstrate that we can utilize the prototype to develop an ensemble relying on fully automated epidemic forecasts (no human intervention) that reaches human-expert level ensemble currently being used by the CDC.

This paper presents the first large-scale multi-species dataset of acoustic recordings of mosquitoes tracked continuously in free flight. We present 20 hours of audio recordings that we have expertly labelled and tagged precisely in time. Significantly, 18 hours of recordings contain annotations from 36 different species. Mosquitoes are well-known carriers of diseases such as malaria, dengue and yellow fever. Collecting this dataset is motivated by the need to assist applications which utilise mosquito acoustics to conduct surveys to help predict outbreaks and inform intervention policy. The task of detecting mosquitoes from the sound of their wingbeats is challenging due to the difficulty in collecting recordings from realistic scenarios. To address this, as part of the HumBug project, we conducted global experiments to record mosquitoes ranging from those bred in culture cages to mosquitoes captured in the wild. Consequently, the audio recordings vary in signal-to-noise ratio and contain a broad range of indoor and outdoor background environments from Tanzania, Thailand, Kenya, the USA and the UK. In this paper we describe in detail how we collected, labelled and curated the data. The data is provided from a PostgreSQL database, which contains important metadata such as the capture method, age, feeding status and gender of the mosquitoes. Additionally, we provide code to extract features and train Bayesian convolutional neural networks for two key tasks: the identification of mosquitoes from their corresponding background environments, and the classification of detected mosquitoes into species. Our extensive dataset is both challenging to machine learning researchers focusing on acoustic identification, and critical to entomologists, geo-spatial modellers and other domain experts to understand mosquito behaviour, model their distribution, and manage the threat they pose to humans.

Dengue fever presents a substantial challenge in developing countries where sanitation infrastructure is inadequate. The absence of comprehensive healthcare systems exacerbates the severity of dengue infections, potentially leading to life-threatening circumstances. Rapid response to dengue outbreaks is also challenging due to limited information exchange and integration. While timely dengue outbreak forecasts have the potential to prevent such outbreaks, the majority of dengue prediction studies have predominantly relied on data that impose significant burdens on individual countries for collection. In this study, our aim is to improve health equity in resource-constrained countries by exploring the effectiveness of high-resolution satellite imagery as a nontraditional and readily accessible data source. By leveraging the wealth of publicly available and easily obtainable satellite imagery, we present a scalable satellite extraction framework based on Sentinel Hub, a cloud-based computing platform. Furthermore, we introduce DengueNet, an innovative architecture that combines Vision Transformer, Radiomics, and Long Short-term Memory to extract and integrate spatiotemporal features from satellite images. This enables dengue predictions on an epi-week basis. To evaluate the effectiveness of our proposed method, we conducted experiments on five municipalities in Colombia. We utilized a dataset comprising 780 high-resolution Sentinel-2 satellite images for training and evaluation. The performance of DengueNet was assessed using the mean absolute error (MAE) metric. Across the five municipalities, DengueNet achieved an average MAE of 43.92. Our findings strongly support the efficacy of satellite imagery as a valuable resource for dengue prediction, particularly in informing public health policies within countries where manually collected data is scarce and dengue virus prevalence is severe.

With people moving out of physical public spaces due to containment measures to tackle the novel coronavirus (COVID-19) pandemic, online platforms become even more prominent tools to understand social discussion. Studying social media can be informative to assess how we are collectively coping with this unprecedented global crisis. However, social media platforms are also populated by bots, automated accounts that can amplify certain topics of discussion at the expense of others. In this paper, we study 43.3M English tweets about COVID-19 and provide early evidence of the use of bots to promote political conspiracies in the United States, in stark contrast with humans who focus on public health concerns.

Training machine learning approaches for vulnerability identification and producing reliable tools to assist developers in implementing quality software -- free of vulnerabilities -- is challenging due to the lack of large datasets and real data. Researchers have been looking at these issues and building datasets. However, these datasets usually miss natural language artifacts and programming language diversity. We scraped the entire CVE details database for GitHub references and augmented the data with 3 security-related datasets. We used the data to create a ground-truth dataset of natural language artifacts (such as commit messages, commits comments, and summaries), meta-data and code changes. Our dataset integrates a total of 8057 security-relevant commits -- the equivalent to 5942 security patches -- from 1339 different projects spanning 146 different types of vulnerabilities and 20 languages. A dataset of 110k non-security-related commits is also provided. Data and scripts are all available on GitHub. Data is stored in a .CSV file. Codebases can be downloaded using our scripts. Our dataset is a valuable asset to answer research questions on different topics such as the identification of security-relevant information using NLP models; software engineering and security best practices; and, vulnerability detection and patching; and, security program analysis.

The acute phase of the Covid-19 pandemic has made apparent the need for decision support based upon accurate epidemic modeling. This process is substantially hampered by under-reporting of cases and related data incompleteness issues. In this article we adopt the Bayesian paradigm and synthesize publicly available data via a discrete-time stochastic epidemic modeling framework. The models allow for estimating the total number of infections while accounting for the endemic phase of the pandemic. We assess the prediction of the infection rate utilizing mobility information, notably the principal components of the mobility data. We evaluate variational Bayes in this context and find that Hamiltonian Monte Carlo offers a robust inference alternative for such models. We elaborate upon vector analysis of the epidemic dynamics, thus enriching the traditional tools used for decision making. In particular, we show how certain 2-dimensional plots on the phase plane may yield intuitive information regarding the speed and the type of transmission dynamics. We investigate the potential of a two-stage analysis as a consequence of cutting feedback, for inference on certain functionals of the model parameters. Finally, we show that a point mass on critical parameters is overly restrictive and investigate informative priors as a suitable alternative.

Systematic literature reviews (SLRs) play an essential role in summarising, synthesising and validating scientific evidence. In recent years, there has been a growing interest in using machine learning techniques to automate the identification of relevant studies for SLRs. However, the lack of standardised evaluation datasets makes comparing the performance of such automated literature screening systems difficult. In this paper, we analyse the citation screening evaluation datasets, revealing that many of the available datasets are either too small, suffer from data leakage or have limited applicability to systems treating automated literature screening as a classification task, as opposed to, for example, a retrieval or question-answering task. To address these challenges, we introduce CSMeD, a meta-dataset consolidating nine publicly released collections, providing unified access to 325 SLRs from the fields of medicine and computer science. CSMeD serves as a comprehensive resource for training and evaluating the performance of automated citation screening models. Additionally, we introduce CSMeD-FT, a new dataset designed explicitly for evaluating the full text publication screening task. To demonstrate the utility of CSMeD, we conduct experiments and establish baselines on new datasets.

To assess the effectiveness of any medical intervention, researchers must conduct a time-intensive and highly manual literature review. NLP systems can help to automate or assist in parts of this expensive process. In support of this goal, we release MS^2 (Multi-Document Summarization of Medical Studies), a dataset of over 470k documents and 20k summaries derived from the scientific literature. This dataset facilitates the development of systems that can assess and aggregate contradictory evidence across multiple studies, and is the first large-scale, publicly available multi-document summarization dataset in the biomedical domain. We experiment with a summarization system based on BART, with promising early results. We formulate our summarization inputs and targets in both free text and structured forms and modify a recently proposed metric to assess the quality of our system's generated summaries. Data and models are available at https://github.com/allenai/ms2

We present a new challenging dataset, CPPE - 5 (Medical Personal Protective Equipment), with the goal to allow the study of subordinate categorization of medical personal protective equipments, which is not possible with other popular data sets that focus on broad-level categories (such as PASCAL VOC, ImageNet, Microsoft COCO, OpenImages, etc). To make it easy for models trained on this dataset to be used in practical scenarios in complex scenes, our dataset mainly contains images that show complex scenes with several objects in each scene in their natural context. The image collection for this dataset focuses on: obtaining as many non-iconic images as possible and making sure all the images are real-life images, unlike other existing datasets in this area. Our dataset includes 5 object categories (coveralls, face shields, gloves, masks, and goggles), and each image is annotated with a set of bounding boxes and positive labels. We present a detailed analysis of the dataset in comparison to other popular broad category datasets as well as datasets focusing on personal protective equipments, we also find that at present there exist no such publicly available datasets. Finally, we also analyze performance and compare model complexities on baseline and state-of-the-art models for bounding box results. Our code, data, and trained models are available at https://git.io/cppe5-dataset.