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Interpreting electrocardiograms (ECGs) and generating comprehensive reports remain challenging tasks in cardiology, often requiring specialized expertise and significant time investment. To address these critical issues, we propose ECG-ReGen, a retrieval-based approach for ECG-to-text report generation and question answering. Our method leverages a self-supervised learning for the ECG encoder, enabling efficient similarity searches and report retrieval. By combining pre-training with dynamic retrieval and Large Language Model (LLM)-based refinement, ECG-ReGen effectively analyzes ECG data and answers related queries, with the potential of improving patient care. Experiments conducted on the PTB-XL and MIMIC-IV-ECG datasets demonstrate superior performance in both in-domain and cross-domain scenarios for report generation. Furthermore, our approach exhibits competitive performance on ECG-QA dataset compared to fully supervised methods when utilizing off-the-shelf LLMs for zero-shot question answering. This approach, effectively combining self-supervised encoder and LLMs, offers a scalable and efficient solution for accurate ECG interpretation, holding significant potential to enhance clinical decision-making.

Respiratory audio, such as coughing and breathing sounds, has predictive power for a wide range of healthcare applications, yet is currently under-explored. The main problem for those applications arises from the difficulty in collecting large labeled task-specific data for model development. Generalizable respiratory acoustic foundation models pretrained with unlabeled data would offer appealing advantages and possibly unlock this impasse. However, given the safety-critical nature of healthcare applications, it is pivotal to also ensure openness and replicability for any proposed foundation model solution. To this end, we introduce OPERA, an OPEn Respiratory Acoustic foundation model pretraining and benchmarking system, as the first approach answering this need. We curate large-scale respiratory audio datasets (~136K samples, 440 hours), pretrain three pioneering foundation models, and build a benchmark consisting of 19 downstream respiratory health tasks for evaluation. Our pretrained models demonstrate superior performance (against existing acoustic models pretrained with general audio on 16 out of 19 tasks) and generalizability (to unseen datasets and new respiratory audio modalities). This highlights the great promise of respiratory acoustic foundation models and encourages more studies using OPERA as an open resource to accelerate research on respiratory audio for health. The system is accessible from https://github.com/evelyn0414/OPERA.

Federated Learning (FL) enables model development by leveraging data distributed across numerous edge devices without transferring local data to a central server. However, existing FL methods still face challenges when dealing with scarce and label-skewed data across devices, resulting in local model overfitting and drift, consequently hindering the performance of the global model. In response to these challenges, we propose a pioneering framework called FLea, incorporating the following key components: i) A global feature buffer that stores activation-target pairs shared from multiple clients to support local training. This design mitigates local model drift caused by the absence of certain classes; ii) A feature augmentation approach based on local and global activation mix-ups for local training. This strategy enlarges the training samples, thereby reducing the risk of local overfitting; iii) An obfuscation method to minimize the correlation between intermediate activations and the source data, enhancing the privacy of shared features. To verify the superiority of FLea, we conduct extensive experiments using a wide range of data modalities, simulating different levels of local data scarcity and label skew. The results demonstrate that FLea consistently outperforms state-of-the-art FL counterparts (among 13 of the experimented 18 settings, the improvement is over 5% while concurrently mitigating the privacy vulnerabilities associated with shared features. Code is available at https://github.com/XTxiatong/FLea.git., Comment: This work was intended as a replacement of arXiv:2312.02327 and any subsequent updates will appear there

Federated Learning (FL) enables model development by leveraging data distributed across numerous edge devices without transferring local data to a central server. However, existing FL methods still face challenges when dealing with scarce and label-skewed data across devices, resulting in local model overfitting and drift, consequently hindering the performance of the global model. In response to these challenges, we propose a pioneering framework called \textit{FLea}, incorporating the following key components: \textit{i)} A global feature buffer that stores activation-target pairs shared from multiple clients to support local training. This design mitigates local model drift caused by the absence of certain classes; \textit{ii)} A feature augmentation approach based on local and global activation mix-ups for local training. This strategy enlarges the training samples, thereby reducing the risk of local overfitting; \textit{iii)} An obfuscation method to minimize the correlation between intermediate activations and the source data, enhancing the privacy of shared features. To verify the superiority of \textit{FLea}, we conduct extensive experiments using a wide range of data modalities, simulating different levels of local data scarcity and label skew. The results demonstrate that \textit{FLea} consistently outperforms state-of-the-art FL counterparts (among 13 of the experimented 18 settings, the improvement is over $5\%$) while concurrently mitigating the privacy vulnerabilities associated with shared features. Code is available at https://github.com/XTxiatong/FLea.git, Comment: This paper has been acceped by KDD'24

Built environment supports all the daily activities and shapes our health. Leveraging informative street view imagery, previous research has established the profound correlation between the built environment and chronic, non-communicable diseases; however, predicting the exposure risk of infectious diseases remains largely unexplored. The person-to-person contacts and interactions contribute to the complexity of infectious disease, which is inherently different from non-communicable diseases. Besides, the complex relationships between street view imagery and epidemic exposure also hinder accurate predictions. To address these problems, we construct a regional mobility graph informed by the gravity model, based on which we propose a transmission-aware graph convolutional network (GCN) to capture disease transmission patterns arising from human mobility. Experiments show that the proposed model significantly outperforms baseline models by 8.54% in weighted F1, shedding light on a low-cost, scalable approach to assess epidemic exposure risks from street view imagery., Comment: Published in ACM SIGSPATIAL 2023

How can we ensure that Ubiquitous Computing (UbiComp) research outcomes are both ethical and fair? While fairness in machine learning (ML) has gained traction in recent years, fairness in UbiComp remains unexplored. This workshop aims to discuss fairness in UbiComp research and its social, technical, and legal implications. From a social perspective, we will examine the relationship between fairness and UbiComp research and identify pathways to ensure that ubiquitous technologies do not cause harm or infringe on individual rights. From a technical perspective, we will initiate a discussion on data practices to develop bias mitigation approaches tailored to UbiComp research. From a legal perspective, we will examine how new policies shape our community's work and future research. We aim to foster a vibrant community centered around the topic of responsible UbiComp, while also charting a clear path for future research endeavours in this field.

Federated learning (FL) aided health diagnostic models can incorporate data from a large number of personal edge devices (e.g., mobile phones) while keeping the data local to the originating devices, largely ensuring privacy. However, such a cross-device FL approach for health diagnostics still imposes many challenges due to both local data imbalance (as extreme as local data consists of a single disease class) and global data imbalance (the disease prevalence is generally low in a population). Since the federated server has no access to data distribution information, it is not trivial to solve the imbalance issue towards an unbiased model. In this paper, we propose FedLoss, a novel cross-device FL framework for health diagnostics. Here the federated server averages the models trained on edge devices according to the predictive loss on the local data, rather than using only the number of samples as weights. As the predictive loss better quantifies the data distribution at a device, FedLoss alleviates the impact of data imbalance. Through a real-world dataset on respiratory sound and symptom-based COVID-$19$ detection task, we validate the superiority of FedLoss. It achieves competitive COVID-$19$ detection performance compared to a centralised model with an AUC-ROC of $79\%$. It also outperforms the state-of-the-art FL baselines in sensitivity and convergence speed. Our work not only demonstrates the promise of federated COVID-$19$ detection but also paves the way to a plethora of mobile health model development in a privacy-preserving fashion., Comment: This paper has been accepted by IEEE ICASSP 2023

Context-aware decision support in the operating room can foster surgical safety and efficiency by leveraging real-time feedback from surgical workflow analysis. Most existing works recognize surgical activities at a coarse-grained level, such as phases, steps or events, leaving out fine-grained interaction details about the surgical activity; yet those are needed for more helpful AI assistance in the operating room. Recognizing surgical actions as triplets of combination delivers comprehensive details about the activities taking place in surgical videos. This paper presents CholecTriplet2021: an endoscopic vision challenge organized at MICCAI 2021 for the recognition of surgical action triplets in laparoscopic videos. The challenge granted private access to the large-scale CholecT50 dataset, which is annotated with action triplet information. In this paper, we present the challenge setup and assessment of the state-of-the-art deep learning methods proposed by the participants during the challenge. A total of 4 baseline methods from the challenge organizers and 19 new deep learning algorithms by competing teams are presented to recognize surgical action triplets directly from surgical videos, achieving mean average precision (mAP) ranging from 4.2% to 38.1%. This study also analyzes the significance of the results obtained by the presented approaches, performs a thorough methodological comparison between them, in-depth result analysis, and proposes a novel ensemble method for enhanced recognition. Our analysis shows that surgical workflow analysis is not yet solved, and also highlights interesting directions for future research on fine-grained surgical activity recognition which is of utmost importance for the development of AI in surgery., Comment: CholecTriplet2021 challenge report. Paper accepted at Elsevier journal of Medical Image Analysis. 22 pages, 8 figures, 11 tables. Challenge website: https://cholectriplet2021.grand-challenge.org

The COVID-19 pandemic has caused massive humanitarian and economic damage. Teams of scientists from a broad range of disciplines have searched for methods to help governments and communities combat the disease. One avenue from the machine learning field which has been explored is the prospect of a digital mass test which can detect COVID-19 from infected individuals' respiratory sounds. We present a summary of the results from the INTERSPEECH 2021 Computational Paralinguistics Challenges: COVID-19 Cough, (CCS) and COVID-19 Speech, (CSS)., Comment: 18 pages, 13 figures

Recent work has shown the potential of using audio data (eg, cough, breathing, and voice) in the screening for COVID-19. However, these approaches only focus on one-off detection and detect the infection given the current audio sample, but do not monitor disease progression in COVID-19. Limited exploration has been put forward to continuously monitor COVID-19 progression, especially recovery, through longitudinal audio data. Tracking disease progression characteristics could lead to more timely treatment. The primary objective of this study is to explore the potential of longitudinal audio samples over time for COVID-19 progression prediction and, especially, recovery trend prediction using sequential deep learning techniques. Crowdsourced respiratory audio data, including breathing, cough, and voice samples, from 212 individuals over 5-385 days were analyzed. We developed a deep learning-enabled tracking tool using gated recurrent units (GRUs) to detect COVID-19 progression by exploring the audio dynamics of the individuals' historical audio biomarkers. The investigation comprised 2 parts: (1) COVID-19 detection in terms of positive and negative (healthy) tests, and (2) longitudinal disease progression prediction over time in terms of probability of positive tests. The strong performance for COVID-19 detection, yielding an AUROC of 0.79, a sensitivity of 0.75, and a specificity of 0.71 supported the effectiveness of the approach compared to methods that do not leverage longitudinal dynamics. We further examined the predicted disease progression trajectory, displaying high consistency with test results with a correlation of 0.75 in the test cohort and 0.86 in a subset of the test cohort who reported recovery. Our findings suggest that monitoring COVID-19 evolution via longitudinal audio data has potential in the tracking of individuals' disease progression and recovery., Comment: Updated title. Revised format according to journal requirements

A biosignal is a signal that can be continuously measured from human bodies, such as respiratory sounds, heart activity (ECG), brain waves (EEG), etc, based on which, machine learning models have been developed with very promising performance for automatic disease detection and health status monitoring. However, dataset shift, i.e., data distribution of inference varies from the distribution of the training, is not uncommon for real biosignal-based applications. To improve the robustness, probabilistic models with uncertainty quantification are adapted to capture how reliable a prediction is. Yet, assessing the quality of the estimated uncertainty remains a challenge. In this work, we propose a framework to evaluate the capability of the estimated uncertainty in capturing different types of biosignal dataset shifts with various degrees. In particular, we use three classification tasks based on respiratory sounds and electrocardiography signals to benchmark five representative uncertainty quantification methods. Extensive experiments show that, although Ensemble and Bayesian models could provide relatively better uncertainty estimations under dataset shifts, all tested models fail to meet the promise in trustworthy prediction and model calibration. Our work paves the way for a comprehensive evaluation for any newly developed biosignal classifiers., Comment: Accepted by The 6th International Workshop on Health Intelligence (W3PHIAI-22)

PURPOSE: Surgical workflow and skill analysis are key technologies for the next generation of cognitive surgical assistance systems. These systems could increase the safety of the operation through context-sensitive warnings and semi-autonomous robotic assistance or improve training of surgeons via data-driven feedback. In surgical workflow analysis up to 91% average precision has been reported for phase recognition on an open data single-center dataset. In this work we investigated the generalizability of phase recognition algorithms in a multi-center setting including more difficult recognition tasks such as surgical action and surgical skill. METHODS: To achieve this goal, a dataset with 33 laparoscopic cholecystectomy videos from three surgical centers with a total operation time of 22 hours was created. Labels included annotation of seven surgical phases with 250 phase transitions, 5514 occurences of four surgical actions, 6980 occurences of 21 surgical instruments from seven instrument categories and 495 skill classifications in five skill dimensions. The dataset was used in the 2019 Endoscopic Vision challenge, sub-challenge for surgical workflow and skill analysis. Here, 12 teams submitted their machine learning algorithms for recognition of phase, action, instrument and/or skill assessment. RESULTS: F1-scores were achieved for phase recognition between 23.9% and 67.7% (n=9 teams), for instrument presence detection between 38.5% and 63.8% (n=8 teams), but for action recognition only between 21.8% and 23.3% (n=5 teams). The average absolute error for skill assessment was 0.78 (n=1 team). CONCLUSION: Surgical workflow and skill analysis are promising technologies to support the surgical team, but are not solved yet, as shown by our comparison of algorithms. This novel benchmark can be used for comparable evaluation and validation of future work.

Fine-grained population distribution data is of great importance for many applications, e.g., urban planning, traffic scheduling, epidemic modeling, and risk control. However, due to the limitations of data collection, including infrastructure density, user privacy, and business security, such fine-grained data is hard to collect and usually, only coarse-grained data is available. Thus, obtaining fine-grained population distribution from coarse-grained distribution becomes an important problem. To tackle this problem, existing methods mainly rely on sufficient fine-grained ground truth for training, which is not often available for the majority of cities. That limits the applications of these methods and brings the necessity to transfer knowledge between data-sufficient source cities to data-scarce target cities. In knowledge transfer scenario, we employ single reference fine-grained ground truth in target city, which is easy to obtain via remote sensing or questionnaire, as the ground truth to inform the large-scale urban structure and support the knowledge transfer in target city. By this approach, we transform the fine-grained population mapping problem into a one-shot transfer learning problem. In this paper, we propose a novel one-shot transfer learning framework PSRNet to transfer spatial-temporal knowledge across cities from the view of network structure, the view of data, and the view of optimization. Experiments on real-life datasets of 4 cities demonstrate that PSRNet has significant advantages over 8 state-of-the-art baselines by reducing RMSE and MAE by more than 25%. Our code and datasets are released in Github (https://github.com/erzhuoshao/PSRNet-CIKM)., Comment: Published in Proceedings of the 30th ACM International Conference on Information and Knowledge Management (CIKM '21)

Recent technology development brings the booming of numerous new Demand-Driven Services (DDS) into urban lives, including ridesharing, on-demand delivery, express systems and warehousing. In DDS, a service loop is an elemental structure, including its service worker, the service providers and corresponding service targets. The service workers should transport either humans or parcels from the providers to the target locations. Various planning tasks within DDS can thus be classified into two individual stages: 1) Dispatching, which is to form service loops from demand/supply distributions, and 2)Routing, which is to decide specific serving orders within the constructed loops. Generating high-quality strategies in both stages is important to develop DDS but faces several challenging. Meanwhile, deep reinforcement learning (DRL) has been developed rapidly in recent years. It is a powerful tool to solve these problems since DRL can learn a parametric model without relying on too many problem-based assumptions and optimize long-term effect by learning sequential decisions. In this survey, we first define DDS, then highlight common applications and important decision/control problems within. For each problem, we comprehensively introduce the existing DRL solutions. We also introduce open simulation environments for development and evaluation of DDS applications. Finally, we analyze remaining challenges and discuss further research opportunities in DRL solutions for DDS., Comment: 21 pages. survey preprint

Researchers have been battling with the question of how we can identify Coronavirus disease (COVID-19) cases efficiently, affordably and at scale. Recent work has shown how audio based approaches, which collect respiratory audio data (cough, breathing and voice) can be used for testing, however there is a lack of exploration of how biases and methodological decisions impact these tools' performance in practice. In this paper, we explore the realistic performance of audio-based digital testing of COVID-19. To investigate this, we collected a large crowdsourced respiratory audio dataset through a mobile app, alongside recent COVID-19 test result and symptoms intended as a ground truth. Within the collected dataset, we selected 5,240 samples from 2,478 participants and split them into different participant-independent sets for model development and validation. Among these, we controlled for potential confounding factors (such as demographics and language). The unbiased model takes features extracted from breathing, coughs, and voice signals as predictors and yields an AUC-ROC of 0.71 (95\% CI: 0.65$-$0.77). We further explore different unbalanced distributions to show how biases and participant splits affect performance. Finally, we discuss how the realistic model presented could be integrated in clinical practice to realize continuous, ubiquitous, sustainable and affordable testing at population scale.

Recently, sound-based COVID-19 detection studies have shown great promise to achieve scalable and prompt digital pre-screening. However, there are still two unsolved issues hindering the practice. First, collected datasets for model training are often imbalanced, with a considerably smaller proportion of users tested positive, making it harder to learn representative and robust features. Second, deep learning models are generally overconfident in their predictions. Clinically, false predictions aggravate healthcare costs. Estimation of the uncertainty of screening would aid this. To handle these issues, we propose an ensemble framework where multiple deep learning models for sound-based COVID-19 detection are developed from different but balanced subsets from original data. As such, data are utilized more effectively compared to traditional up-sampling and down-sampling approaches: an AUC of 0.74 with a sensitivity of 0.68 and a specificity of 0.69 is achieved. Simultaneously, we estimate uncertainty from the disagreement across multiple models. It is shown that false predictions often yield higher uncertainty, enabling us to suggest the users with certainty higher than a threshold to repeat the audio test on their phones or to take clinical tests if digital diagnosis still fails. This study paves the way for a more robust sound-based COVID-19 automated screening system., Comment: Accepted by INTERSPEECH 2021

The INTERSPEECH 2021 Computational Paralinguistics Challenge addresses four different problems for the first time in a research competition under well-defined conditions: In the COVID-19 Cough and COVID-19 Speech Sub-Challenges, a binary classification on COVID-19 infection has to be made based on coughing sounds and speech; in the Escalation SubChallenge, a three-way assessment of the level of escalation in a dialogue is featured; and in the Primates Sub-Challenge, four species vs background need to be classified. We describe the Sub-Challenges, baseline feature extraction, and classifiers based on the 'usual' COMPARE and BoAW features as well as deep unsupervised representation learning using the AuDeep toolkit, and deep feature extraction from pre-trained CNNs using the Deep Spectrum toolkit; in addition, we add deep end-to-end sequential modelling, and partially linguistic analysis., Comment: 5 pages

The development of fast and accurate screening tools, which could facilitate testing and prevent more costly clinical tests, is key to the current pandemic of COVID-19. In this context, some initial work shows promise in detecting diagnostic signals of COVID-19 from audio sounds. In this paper, we propose a voice-based framework to automatically detect individuals who have tested positive for COVID-19. We evaluate the performance of the proposed framework on a subset of data crowdsourced from our app, containing 828 samples from 343 participants. By combining voice signals and reported symptoms, an AUC of $0.79$ has been attained, with a sensitivity of $0.68$ and a specificity of $0.82$. We hope that this study opens the door to rapid, low-cost, and convenient pre-screening tools to automatically detect the disease., Comment: 5 pages, 3 figures, 2 tables, Accepted for publication at ICASSP 2021

The recent outbreak of COVID-19 poses a serious threat to people's lives. Epidemic control strategies have also caused damage to the economy by cutting off humans' daily commute. In this paper, we develop an Individual-based Reinforcement Learning Epidemic Control Agent (IDRLECA) to search for smart epidemic control strategies that can simultaneously minimize infections and the cost of mobility intervention. IDRLECA first hires an infection probability model to calculate the current infection probability of each individual. Then, the infection probabilities together with individuals' health status and movement information are fed to a novel GNN to estimate the spread of the virus through human contacts. The estimated risks are used to further support an RL agent to select individual-level epidemic-control actions. The training of IDRLECA is guided by a specially designed reward function considering both the cost of mobility intervention and the effectiveness of epidemic control. Moreover, we design a constraint for control-action selection that eases its difficulty and further improve exploring efficiency. Extensive experimental results demonstrate that IDRLECA can suppress infections at a very low level and retain more than 95% of human mobility.

A considerable amount of mobility data has been accumulated due to the proliferation of location-based service. Nevertheless, compared with mobility data from transportation systems like the GPS module in taxis, this kind of data is commonly sparse in terms of individual trajectories in the sense that users do not access mobile services and contribute their data all the time. Consequently, the sparsity inevitably weakens the practical value of the data even it has a high user penetration rate. To solve this problem, we propose a novel attentional neural network-based model, named AttnMove, to densify individual trajectories by recovering unobserved locations at a fine-grained spatial-temporal resolution. To tackle the challenges posed by sparsity, we design various intra- and inter- trajectory attention mechanisms to better model the mobility regularity of users and fully exploit the periodical pattern from long-term history. We evaluate our model on two real-world datasets, and extensive results demonstrate the performance gain compared with the state-of-the-art methods. This also shows that, by providing high-quality mobility data, our model can benefit a variety of mobility-oriented down-stream applications.

Audio signals generated by the human body (e.g., sighs, breathing, heart, digestion, vibration sounds) have routinely been used by clinicians as indicators to diagnose disease or assess disease progression. Until recently, such signals were usually collected through manual auscultation at scheduled visits. Research has now started to use digital technology to gather bodily sounds (e.g., from digital stethoscopes) for cardiovascular or respiratory examination, which could then be used for automatic analysis. Some initial work shows promise in detecting diagnostic signals of COVID-19 from voice and coughs. In this paper we describe our data analysis over a large-scale crowdsourced dataset of respiratory sounds collected to aid diagnosis of COVID-19. We use coughs and breathing to understand how discernible COVID-19 sounds are from those in asthma or healthy controls. Our results show that even a simple binary machine learning classifier is able to classify correctly healthy and COVID-19 sounds. We also show how we distinguish a user who tested positive for COVID-19 and has a cough from a healthy user with a cough, and users who tested positive for COVID-19 and have a cough from users with asthma and a cough. Our models achieve an AUC of above 80% across all tasks. These results are preliminary and only scratch the surface of the potential of this type of data and audio-based machine learning. This work opens the door to further investigation of how automatically analysed respiratory patterns could be used as pre-screening signals to aid COVID-19 diagnosis., Comment: 9 pages, 6 figures, 2 tables, Accepted for publication at KDD'20 (Health Day)

Understanding urban dynamics, i.e., how the types and intensity of urban residents' activities in the city change along with time, is of urgent demand for building an efficient and livable city. Nonetheless, this is challenging due to the expanding urban population and the complicated spatial distribution of residents. In this paper, to reveal urban dynamics, we propose a novel system UrbanRhythm to reveal the urban dynamics hidden in human mobility data. UrbanRhythm addresses three questions: 1) What mobility feature should be used to present residents' high-dimensional activities in the city? 2) What are basic components of urban dynamics? 3) What are the long-term periodicity and short-term regularity of urban dynamics? In UrbanRhythm, we extract staying, leaving, arriving three attributes of mobility and use a image processing method Saak transform to calculate the mobility distribution feature. For the second question, several city states are identified by hierarchy clustering as the basic components of urban dynamics, such as sleeping states and working states. We further characterize the urban dynamics as the transform of city states along time axis. For the third question, we directly observe the long-term periodicity of urban dynamics from visualization. Then for the short-term regularity, we design a novel motif analysis method to discovery motifs as well as their hierarchy relationships. We evaluate our proposed system on two real-life datesets and validate the results according to App usage records. This study sheds light on urban dynamics hidden in human mobility and can further pave the way for more complicated mobility behavior modeling and deeper urban understanding., Comment: Submitted to IEEE Transactions on Knowledge and Data Engineering (TKDE)