PANDEM-Source, a tool to collect or generate surveillance indicators for pandemic management: a use case with COVID-19 data

Introduction

PANDEM-Source (PS) is a tool to collect and integrate openly available public health-related data from heterogeneous data sources to support the surveillance of infectious diseases for pandemic management. The tool may also be used for pandemic preparedness by generating surveillance data for training purposes. It was developed as part of the EU-funded Horizon 2020 PANDEM-2 project during the COVID-19 pandemic as a result of close collaboration in a consortium of 19 partners, including six European public health agencies, one hospital, and three first responder organizations. This manuscript describes PS's features and design to disseminate its characteristics and capabilities to strengthen pandemic preparedness and response.

Methods

A requirement-gathering process with EU pandemic managers in the consortium was performed to identify and prioritize a list of variables and indicators useful for surveillance and pandemic management. Using the COVID-19 pandemic as a use case, we developed PS with the purpose of feeding all necessary data to be displayed in the PANDEM-2 dashboard.

Results

PS routinely monitors, collects, and standardizes data from open or restricted heterogeneous data sources (users can upload their own data). It supports indicators and health resources related data from traditional data sources reported by national and international agencies, and indicators from non-traditional data sources such as those captured in social and mass media, participatory surveillance, and seroprevalence studies. The tool can also calculate indicators and be used to produce data for training purposes by generating synthetic data from a minimal set of indicators to simulate pandemic scenarios. PS is currently set up for COVID-19 surveillance at the European level but can be adapted to other diseases or threats and regions.

Conclusion

With the lessons learnt during the COVID-19 pandemic, it is important to keep building capacity to monitor potential threats and develop tools that can facilitate training in all the necessary aspects to manage future pandemics. PS is open source and its design provides flexibility to collect heterogeneous data from open data sources or to upload end users's own data and customize surveillance indicators. PS is easily adaptable to future threats or different training scenarios. All these features make PS a unique and valuable tool for pandemic management.

The wisdom of claiming ownership of human genomic data: A cautionary tale for research institutions

This article considers the practical question of how research institutions should best structure their legal relationship with the human genomic data that they generate. The analysis, based on South African law, is framed by the legal position that although a research institution that generates human genomic data is not automatically the owner thereof, it is well positioned to claim ownership of newly generated data instances. Given that the research institution exerts effort to generate the data, it can be argued that it has a moral right to claim ownership of such data. Combined with the fact that it has an interest in having comprehensive rights in such data, it appears that the prudent policy for research institutions is to claim ownership of the human genomic data instances that they generate. This policy is tested against two opposing policy positions. The first opposing policy position is that research participants should own the data that relate to them. However, in light of data protection legislation that already provides extensive protections to research participants, bestowing data ownership on research participants would offer little benefit to such individuals, while leading to significant practical problems for research institutions. The second opposing policy position is that the concept of ownership should be abandoned in favour of data custodianship. This opposing position is problematic, as avoiding reference to ownership is a denial of legal reality and hence not a useful policy. Also, avoiding reference to ownership will leave research institutions with limited legal remedies in the event of appropriation of data by third parties. Accordingly, it is concluded that the wisest policy for research institutions is indeed to explicitly claim ownership of the human genomic data instances that they generate.

A Fault Diagnosis Strategy for Analog Circuits with Limited Samples Based on the Combination of the Transformer and Generative Models

As a pivotal integral component within electronic systems, analog circuits are of paramount importance for the timely detection and precise diagnosis of their faults. However, the objective reality of limited fault samples in operational devices with analog circuitry poses challenges to the direct applicability of existing diagnostic methods. This study proposes an innovative approach for fault diagnosis in analog circuits by integrating deep convolutional generative adversarial networks (DCGANs) with the Transformer architecture, addressing the problem of insufficient fault samples affecting diagnostic performance. Firstly, the employment of the continuous wavelet transform in combination with Morlet wavelet basis functions serves as a means to derive time-frequency images, enhancing fault feature recognition while converting time-domain signals into time-frequency representations. Furthermore, the augmentation of datasets utilizing deep convolutional GANs is employed to generate synthetic time-frequency signals from existing fault data. The Transformer-based fault diagnosis model was trained using a mixture of original signals and generated signals, and the model was subsequently tested. Through experiments involving single and multiple fault scenarios in three simulated circuits, a comparative analysis of the proposed approach was conducted with a number of established benchmark methods, and its effectiveness in various scenarios was evaluated. In addition, the ability of the proposed fault diagnosis technique was investigated in the presence of limited fault data samples. The outcome reveals that the proposed diagnostic method exhibits a consistently high overall accuracy of over 96% in diverse test scenarios. Moreover, it delivers satisfactory performance even when real sample sizes are as small as 150 instances in various fault categories.

Digital Phenotyping for Monitoring and Disease Trajectory Prediction of Patients With Cancer: Protocol for a Prospective Observational Cohort Study

BACKGROUND

Timely recognition of cancer progression and treatment complications is important for treatment guidance. Digital phenotyping is a promising method for precise and remote monitoring of patients in their natural environments by using passively generated data from sensors of personal wearable devices. Further studies are needed to better understand the potential clinical benefits of digital phenotyping approaches to optimize care of patients with cancer.

OBJECTIVE

We aim to evaluate whether passively generated data from smartphone sensors are feasible for remote monitoring of patients with cancer to predict their disease trajectories and patient-centered health outcomes.

METHODS

We will recruit 200 patients undergoing treatment for cancer. Patients will be followed up for 6 months. Passively generated data by sensors of personal smartphone devices (eg, accelerometer, gyroscope, GPS) will be continuously collected using the developed LAIMA smartphone app during follow-up. We will evaluate (1) mobility data by using an accelerometer (mean time of active period, mean time of exertional physical activity, distance covered per day, duration of inactive period), GPS (places of interest visited daily, hospital visits), and gyroscope sensors and (2) sociability indices (frequency of duration of phone calls, frequency and length of text messages, and internet browsing time). Every 2 weeks, patients will be asked to complete questionnaires pertaining to quality of life (European Organization for Research and Treatment of Cancer Core Quality of Life Questionnaire [EORTC QLQ-C30]), depression symptoms (Patient Health Questionnaire-9 [PHQ-9]), and anxiety symptoms (General Anxiety Disorder-7 [GAD-7]) that will be deployed via the LAIMA app. Clinic visits will take place at 1-3 months and 3-6 months of the study. Patients will be evaluated for disease progression, cancer and treatment complications, and functional status (Eastern Cooperative Oncology Group) by the study oncologist and will complete the questionnaire for evaluating quality of life (EORTC QLQ-C30), depression symptoms (PHQ-9), and anxiety symptoms (GAD-7). We will examine the associations among digital, clinical, and patient-reported health outcomes to develop prediction models with clinically meaningful outcomes.

RESULTS

As of July 2023, we have reached the planned recruitment target, and patients are undergoing follow-up. Data collection is expected to be completed by September 2023. The final results should be available within 6 months after study completion.

CONCLUSIONS

This study will provide in-depth insight into temporally and spatially precise trajectories of patients with cancer that will provide a novel digital health approach and will inform the design of future interventional clinical trials in oncology. Our findings will allow a better understanding of the potential clinical value of passively generated smartphone sensor data (digital phenotyping) for continuous and real-time monitoring of patients with cancer for treatment side effects, cancer complications, functional status, and patient-reported outcomes as well as prediction of disease progression or trajectories.

INTERNATIONAL REGISTERED REPORT IDENTIFIER (IRRID)

PRR1-10.2196/49096.

GPU Rasterization-Based 3D LiDAR Simulation for Deep Learning

High-quality data are of utmost importance for any deep-learning application. However, acquiring such data and their annotation is challenging. This paper presents a GPU-accelerated simulator that enables the generation of high-quality, perfectly labelled data for any Time-of-Flight sensor, including LiDAR. Our approach optimally exploits the 3D graphics pipeline of the GPU, significantly decreasing data generation time while preserving compatibility with all real-time rendering engines. The presented algorithms are generic and allow users to perfectly mimic the unique sampling pattern of any such sensor. To validate our simulator, two neural networks are trained for denoising and semantic segmentation. To bridge the gap between reality and simulation, a novel loss function is introduced that requires only a small set of partially annotated real data. It enables the learning of classes for which no labels are provided in the real data, hence dramatically reducing annotation efforts. With this work, we hope to provide means for alleviating the data acquisition problem that is pertinent to deep-learning applications.

Synthetic biomedical data generation in support of In Silico Clinical Trials

Living in the era of Big Data, one may advocate that the additional synthetic generation of data is redundant. However, to be able to truly say whether it is valid or not, one needs to focus more on the meaning and quality of data than on the quantity. In some domains, such as biomedical and translational sciences, data privacy still holds a higher importance than data sharing. This by default limits access to valuable research data. Intensive discussion, agreements, and conventions among different medical research players, as well as effective techniques and regulations for data anonymization, already made a big step toward simplification of data sharing. However, the situation with the availability of data about rare diseases or outcomes of novel treatments still requires costly and risky clinical trials and, thus, would greatly benefit from smart data generation. Clinical trials and tests on animals initiate a cyclic procedure that may involve multiple redesigns and retesting, which typically takes two or three years for medical devices and up to eight years for novel medicines, and costs between 10 and 20 million euros. The US Food and Drug Administration (FDA) acknowledges that for many novel devices, practical limitations require alternative approaches, such as computer modeling and engineering tests, to conduct large, randomized studies. In this article, we give an overview of global initiatives advocating for computer simulations in support of the 3R principles (Replacement, Reduction, and Refinement) in humane experimentation. We also present several research works that have developed methodologies of smart and comprehensive generation of synthetic biomedical data, such as virtual cohorts of patients, in support of In Silico Clinical Trials (ISCT) and discuss their common ground.

Survey of Time Series Data Generation in IoT

Nowadays, with the rapid growth of the internet of things (IoT), massive amounts of time series data are being generated. Time series data play an important role in scientific and technological research for conducting experiments and studies to obtain solid and convincing results. However, due to privacy restrictions, limited access to time series data is always an obstacle. Moreover, the limited available open source data are often not suitable because of a small quantity and insufficient dimensionality and complexity. Therefore, time series data generation has become an imperative and promising solution. In this paper, we provide an overview of classical and state-of-the-art time series data generation methods in IoT. We classify the time series data generation methods into four major categories: rule-based methods, simulation-model-based methods, traditional machine-learning-based methods, and deep-learning-based methods. For each category, we first illustrate its characteristics and then describe the principles and mechanisms of the methods. Finally, we summarize the challenges and future directions of time series data generation in IoT. The systematic classification and evaluation will be a valuable reference for researchers in the time series data generation field.

A framework for selecting data generation strategies in qualitative health research studies

BACKGROUND

Qualitative health research has the potential to answer important applied health research questions to inform nutrition and dietetics practice, education and policy. Qualitative health research is a distinct subdiscipline of qualitative inquiry that purposefully draws upon the context of healthcare and emphasises health and wellness.

METHODS

Qualitative health research is defined by two parameters: (1) the focus of the study and (2) the methods used. When considering the methods to be used, decisions are required about the type of data to be generated (e.g., transcripts, images and notes) and the process involved in data generation (e.g., interviews, elicitation strategies and observations) to answer the research question(s). Drawing upon examples from nutrition and dietetics literature, this paper provides a framework to support decision-making for nutrition and dietetics researchers and clinician researchers designing conducting qualitative health research.

RESULTS

The guiding questions of the framework include: What types of data will be generated? Who is involved in data generation? Where will data generation occur? When will data generation occur? How will data be recorded and managed? and How will participants' and researchers' emotional safety be promoted?

CONCLUSION

Questions about the types of data, those involved, where and when, as well as how safety can be maintained in data generation, not only support a more robust design and description of data generation methods but also keep the person at the centre of the research.

Nighttime Image Dehazing by Render

Nighttime image dehazing presents unique challenges due to the unevenly distributed haze caused by the color change of artificial light sources. This results in multiple interferences, including atmospheric light, glow, and direct light, which make the complex scattering haze interference difficult to accurately distinguish and remove. Additionally, obtaining pairs of high-definition data for fog removal at night is a difficult task. These challenges make nighttime image dehazing a particularly challenging problem to solve. To address these challenges, we introduced the haze scattering formula to more accurately express the haze in three-dimensional space. We also proposed a novel data synthesis method using the latest CG textures and lumen lighting technology to build scenes where various hazes can be seen clearly through ray tracing. We converted the complex 3D scattering relationship transformation into a 2D image dataset to better learn the mapping from 3D haze to 2D haze. Additionally, we improved the existing neural network and established a night haze intensity evaluation label based on the idea of optical PSF. This allowed us to adjust the haze intensity of the rendered dataset according to the intensity of the real haze image and improve the accuracy of dehazing. Our experiments showed that our data construction and network improvement achieved better visual effects, objective indicators, and calculation speed.

Accurate Nonlinearity and Temperature Compensation Method for Piezoresistive Pressure Sensors Based on Data Generation

Piezoresistive pressure sensors exhibit inherent nonlinearity and sensitivity to ambient temperature, requiring multidimensional compensation to achieve accurate measurements. However, recent studies on software compensation mainly focused on developing advanced and intricate algorithms while neglecting the importance of calibration data and the limitation of computing resources. This paper aims to present a novel compensation method which generates more data by learning the calibration process of pressure sensors and uses a larger dataset instead of more complex models to improve the compensation effect. This method is performed by the proposed aquila optimizer optimized mixed polynomial kernel extreme learning machine (AO-MPKELM) algorithm. We conducted a detailed calibration experiment to assess the quality of the generated data and evaluate the performance of the proposed method through ablation analysis. The results demonstrate a high level of consistency between the generated and real data, with a maximum voltage deviation of only 0.71 millivolts. When using a bilinear interpolation algorithm for compensation, extra generated data can help reduce measurement errors by 78.95%, ultimately achieving 0.03% full-scale (FS) accuracy. These findings prove the proposed method is valid for high-accuracy measurements and has superior engineering applicability.

How to train a self-driving vehicle: On the added value (or lack thereof) of curriculum learning and replay buffers

Learning from only real-world collected data can be unrealistic and time consuming in many scenario. One alternative is to use synthetic data as learning environments to learn rare situations and replay buffers to speed up the learning. In this work, we examine the hypothesis of how the creation of the environment affects the training of reinforcement learning agent through auto-generated environment mechanisms. We take the autonomous vehicle as an application. We compare the effect of two approaches to generate training data for artificial cognitive agents. We consider the added value of curriculum learning-just as in human learning-as a way to structure novel training data that the agent has not seen before as well as that of using a replay buffer to train further on data the agent has seen before. In other words, the focus of this paper is on characteristics of the training data rather than on learning algorithms. We therefore use two tasks that are commonly trained early on in autonomous vehicle research: lane keeping and pedestrian avoidance. Our main results show that curriculum learning indeed offers an additional benefit over a vanilla reinforcement learning approach (using Deep-Q Learning), but the replay buffer actually has a detrimental effect in most (but not all) combinations of data generation approaches we considered here. The benefit of curriculum learning does depend on the existence of a well-defined difficulty metric with which various training scenarios can be ordered. In the lane-keeping task, we can define it as a function of the curvature of the road, in which the steeper and more occurring curves on the road, the more difficult it gets. Defining such a difficulty metric in other scenarios is not always trivial. In general, the results of this paper emphasize both the importance of considering data characterization, such as curriculum learning, and the importance of defining an appropriate metric for the task.

Toward global integration of biodiversity big data: a harmonized metabarcode data generation module for terrestrial arthropods

Metazoan metabarcoding is emerging as an essential strategy for inventorying biodiversity, with diverse projects currently generating massive quantities of community-level data. The potential for integrating across such data sets offers new opportunities to better understand biodiversity and how it might respond to global change. However, large-scale syntheses may be compromised if metabarcoding workflows differ from each other. There are ongoing efforts to improve standardization for the reporting of inventory data. However, harmonization at the stage of generating metabarcode data has yet to be addressed. A modular framework for harmonized data generation offers a pathway to navigate the complex structure of terrestrial metazoan biodiversity. Here, through our collective expertise as practitioners, method developers, and researchers leading metabarcoding initiatives to inventory terrestrial biodiversity, we seek to initiate a harmonized framework for metabarcode data generation, with a terrestrial arthropod module. We develop an initial set of submodules covering the 5 main steps of metabarcode data generation: (i) sample acquisition; (ii) sample processing; (iii) DNA extraction; (iv) polymerase chain reaction amplification, library preparation, and sequencing; and (v) DNA sequence and metadata deposition, providing a backbone for a terrestrial arthropod module. To achieve this, we (i) identified key points for harmonization, (ii) reviewed the current state of the art, and (iii) distilled existing knowledge within submodules, thus promoting best practice by providing guidelines and recommendations to reduce the universe of methodological options. We advocate the adoption and further development of the terrestrial arthropod module. We further encourage the development of modules for other biodiversity fractions as an essential step toward large-scale biodiversity synthesis through harmonization.

Generating Synthetic Labeled Data From Existing Anatomical Models: An Example With Echocardiography Segmentation

Deep learning can bring time savings and increased reproducibility to medical image analysis. However, acquiring training data is challenging due to the time-intensive nature of labeling and high inter-observer variability in annotations. Rather than labeling images, in this work we propose an alternative pipeline where images are generated from existing high-quality annotations using generative adversarial networks (GANs). Annotations are derived automatically from previously built anatomical models and are transformed into realistic synthetic ultrasound images with paired labels using a CycleGAN. We demonstrate the pipeline by generating synthetic 2D echocardiography images to compare with existing deep learning ultrasound segmentation datasets. A convolutional neural network is trained to segment the left ventricle and left atrium using only synthetic images. Networks trained with synthetic images were extensively tested on four different unseen datasets of real images with median Dice scores of 91, 90, 88, and 87 for left ventricle segmentation. These results match or are better than inter-observer results measured on real ultrasound datasets and are comparable to a network trained on a separate set of real images. Results demonstrate the images produced can effectively be used in place of real data for training. The proposed pipeline opens the door for automatic generation of training data for many tasks in medical imaging as the same process can be applied to other segmentation or landmark detection tasks in any modality. The source code and anatomical models are available to other researchers.1 1https://adgilbert.github.io/data-generation/.

SpineDepth: A Multi-Modal Data Collection Approach for Automatic Labelling and Intraoperative Spinal Shape Reconstruction Based on RGB-D Data

Computer aided orthopedic surgery suffers from low clinical adoption, despite increased accuracy and patient safety. This can partly be attributed to cumbersome and often radiation intensive registration methods. Emerging RGB-D sensors combined with artificial intelligence data-driven methods have the potential to streamline these procedures. However, developing such methods requires vast amount of data. To this end, a multi-modal approach that enables acquisition of large clinical data, tailored to pedicle screw placement, using RGB-D sensors and a co-calibrated high-end optical tracking system was developed. The resulting dataset comprises RGB-D recordings of pedicle screw placement along with individually tracked ground truth poses and shapes of spine levels L1-L5 from ten cadaveric specimens. Besides a detailed description of our setup, quantitative and qualitative outcome measures are provided. We found a mean target registration error of 1.5 mm. The median deviation between measured and ground truth bone surface was 2.4 mm. In addition, a surgeon rated the overall alignment based on 10% random samples as 5.8 on a scale from 1 to 6. Generation of labeled RGB-D data for orthopedic interventions with satisfactory accuracy is feasible, and its publication shall promote future development of data-driven artificial intelligence methods for fast and reliable intraoperative registration.

ODM Clinical Data Generator: Syntactically Correct Clinical Data Based on Metadata Definition

The Operational Data Model (ODM) is a data standard for interchanging clinical trial data. ODM contains the metadata definition of a study, i.e., case report forms, as well as the clinical data, i.e., the answers of the participants. The portal of medical data models is an infrastructure for creation, exchange, and analysis of medical metadata models. There, over 23000 metadata definitions can be downloaded in ODM format. Due to data protection law and privacy issues, clinical data is not contained in these files. Access to exemplary clinical test data in the desired metadata definition is necessary in order to evaluate systems claiming to support ODM or to evaluate if a planned statistical analysis can be performed with the defined data types. In this work, we present a web application, which generates syntactically correct clinical data in ODM format based on an uploaded ODM metadata definition. Data types and range constraints are taken into account. Data for up to one million participants can be generated in a reasonable amount of time. Thus, in combination with the portal of medical data models, a large number of ODM files including metadata definition and clinical data can be provided for testing of any ODM supporting system. The current version of the application can be tested at https://cdgen.uni-muenster.de and source code is available, under MIT license, at https://imigitlab.uni-muenster.de/published/odm-clinical-data-generator.

Detection of Dementia-Related Abnormal Behaviour Using Recursive Auto-Encoders

Age-related health issues have been increasing with the rise of life expectancy all over the world. One of these problems is cognitive impairment, which causes elderly people to have problems performing their daily activities. Detection of cognitive impairment at an early stage would enable medical doctors to deepen diagnosis and follow-up on patient status. Recent studies show that daily activities can be used to assess the cognitive status of elderly people. Additionally, the intrinsic structure of activities and the relationships between their sub-activities are important clues for capturing the cognitive abilities of seniors. Existing methods perceive each activity as a stand-alone unit while ignoring their inner structural relationships. This study investigates such relationships by modelling activities hierarchically from their sub-activities, with the overall goal of detecting abnormal activities linked to cognitive impairment. For this purpose, recursive auto-encoders (RAE) and their linear vs. greedy and supervised vs. semi-supervised variants are adopted to model the activities. Then, abnormal activities are systematically detected using RAE's reconstruction error. Moreover, to apply RAEs for this problem, we introduce a new sensor representation called raw sensor measurement (RSM) that captures the intrinsic structure of activities, such as the frequency and the order of sensor activations. As real-world data are not accessible, we generated data by simulating abnormal behaviour, which reflects on cognitive impairment. Extensive experiments show that RAEs can be used as a decision-supporting tool, especially when the training set is not labelled to detect early indicators of dementia.

PPGSynth: An Innovative Toolbox for Synthesizing Regular and Irregular Photoplethysmography Waveforms

Photoplethysmography (PPG) is increasingly used in digital health, exceptionally in smartwatches. The PPG signal contains valuable information about heart activity, and there is lots of research interest in its means and analysis for cardiovascular diseases. Unfortunately, to our knowledge, there is no arrhythmic PPG dataset publicly available—this paper attempt to provide a toolbox that can generate synthesized arrhythmic PPG signals. The model of a single PPG pulse in this toolbox utilizes two combined Gaussian functions. This toolbox supports synthesizing PPG waveform with regular heartbeats and three irregular heartbeats: compensation, interpolation, and reset. The user can generate a large amount of PPG data with a certain irregularity, with different sampling frequency, time length, and a range of noise types (Gaussian noise and multi-frequency noise) can be added to the synthesized PPG which can all be modified from the interface, and different types of arrhythmic PPGs (as calculated by the model) generated. The generation for large PPG datasets that simulate PPG collected from real humans could be used for testing the robustness of developed algorithms that are targeting arrhythmic PPG signals. Our PPG synthesis tool is publicly available.

Real-world evidence for coverage decisions: opportunities and challenges

AIM

To explore current uses of real-world evidence (RWE) in the US healthcare system, summarize key concerns and highlight various opportunities that could be realized through best use of RWE. Materials & methods: Information was gathered via a literature review and interviews to generate a background paper for the 2017 Institute for Clinical and Economic Review Policy Summit meeting.

RESULTS

RWE is currently being utilized in drug development decisions, regulatory approval decisions, post-approval monitoring, payer coverage decisions (initial decisions and reassessments) and for outcomes-based contracting. Solutions to key challenges and opportunities for future development are presented.

CONCLUSION

Exciting opportunities for the use of RWE exist, yet important reservations remain. Solutions are within reach if effective partnerships between stakeholders can be nurtured.