Integrated approach to generate artificial samples with low tumor fraction for somatic variant calling benchmarking.

BACKGROUND: High-throughput sequencing (HTS) has become the gold standard approach for variant analysis in cancer research. However, somatic variants may occur at low fractions due to contamination from normal cells or tumor heterogeneity; this poses a significant challenge for standard HTS analysis pipelines. The problem is exacerbated in scenarios with minimal tumor DNA, such as circulating tumor DNA in plasma. Assessing sensitivity and detection of HTS approaches in such cases is paramount, but time-consuming and expensive: specialized experimental protocols and a sufficient quantity of samples are required for processing and analysis. To overcome these limitations, we propose a new computational approach specifically designed for the generation of artificial datasets suitable for this task, simulating ultra-deep targeted sequencing data with low-fraction variants and demonstrating their effectiveness in benchmarking low-fraction variant calling. RESULTS: Our approach enables the generation of artificial raw reads that mimic real data without relying on pre-existing data by using NEAT, a fine-grained read simulator that generates artificial datasets using models learned from multiple different datasets. Then, it incorporates low-fraction variants to simulate somatic mutations in samples with minimal tumor DNA content. To prove the suitability of the created artificial datasets for low-fraction variant calling benchmarking, we used them as ground truth to evaluate the performance of widely-used variant calling algorithms: they allowed us to define tuned parameter values of major variant callers, considerably improving their detection of very low-fraction variants. CONCLUSIONS: Our findings highlight both the pivotal role of our approach in creating adequate artificial datasets with low tumor fraction, facilitating rapid prototyping and benchmarking of algorithms for such dataset type, as well as the important need of advancing low-fraction variant calling techniques.

Comparison of Full-Time Equivalent and Clinic Time Labor Input Measures in Productivity Metrics.

GOAL: A lack of improvement in productivity in recent years may be the result of suboptimal measurement of productivity. Hospitals and clinics benefit from external benchmarks that allow assessment of clinical productivity. Work relative value units have long served as a common currency for this purpose. Productivity is determined by comparing work relative value units to full-time equivalents (FTEs), but FTEs do not have a universal or standardized definition, which could cause problems. We propose a new clinical labor input measure-"clinic time"-as a substitute for using the reported measure of FTEs. METHODS: In this observational validation study, we used data from a cluster randomized trial to compare FTE with clinic time. We compared these two productivity measures graphically. For validation, we estimated two separate ordinary least squares (OLS) regression models. To validate and simultaneously adjust for endogeneity, we used instrumental variables (IV) regression with the proportion of days in a pay period that were federal holidays as an instrument. We used productivity data collected between 2018 and 2020 from Veterans Health Administration (VA) cardiology and orthopedics providers as part of a 2-year cluster randomized trial of medical scribes mandated by the VA Maintaining Internal Systems and Strengthening Integrated Outside Networks (MISSION) Act of 2018. PRINCIPAL FINDINGS: Our cohort included 654 unique providers. For both productivity variables, the values for patients per clinic day were consistently higher than those for patients per day per FTE. To validate these measures, we estimated separate OLS and IV regression models, predicting wait times from the two productivity measures. The slopes from the two productivity measures were positive and small in magnitude with OLS, but negative and large in magnitude with IV regression. The magnitude of the slope for patients per clinic day was much larger than the slope for patients per day per FTE. Current metrics that rely on FTE data may suffer from self-report bias and low reporting frequency. Using clinic time as an alternative is an effective way to mitigate these biases. PRACTICAL APPLICATIONS: Measuring productivity accurately is essential because provider productivity plays an important role in facilitating clinic operations outcomes. Most importantly, tracking a more valid productivity metric is a concrete, cost-effective management tactic to improve the provision of care in the long term.

Extremes of Emergency Department Boarding are Associated With Poorer Financial Performance Among Hospitals.

GOAL: Boarding emergency department (ED) patients is associated with reductions in quality of care, patient safety and experience, and ED operational efficiency. However, ED boarding is ultimately reflective of inefficiencies in hospital capacity management. The ability of a hospital to accommodate variability in patient flow presumably affects its financial performance, but this relationship is not well studied. We investigated the relationship between ED boarding and hospital financial performance measures. Our objective was to see if there was an association between key financial measures of business performance and limitations in patient progression efficiency, as evidenced by ED boarding. METHODS: Cross-sectional ED operational data were collected from the Emergency Department Benchmarking Alliance, a voluntarily self-reporting operational database that includes 54% of EDs in the United States. Freestanding EDs, pediatric EDs and EDs with missing boarding data were excluded. The key operational outcome variable was boarding time. We reviewed the financial information of these nonprofit institutions by accessing their Internal Revenue Service Form 990. We examined standard measures of financial performance, including return on equity, total margin, total asset turnover, and equity multiplier (EM). We studied these associations using quantile regressions of added ED volume, ED admission percentage, urban versus nonurban ED site location, trauma status, and percentage of the population receiving Medicare and Medicaid as covariates in the regression models. PRINCIPAL FINDINGS: Operational data were available for 892 EDs from 31 states. Of those, 127 reported a Form 990 in the year corresponding to the ED boarding measures. Median boarding time across EDs was 148 min (interquartile range [IQR]: 100-216). A significant relationship exists between boarding and the EM, along with a negative association with the hospital's total profit margin in the highest-performing hospitals (by profit margin percentage). After adjusting for the covariates in the regression model, we found that for every 10 min above 90 min of boarding, the mean EM for the top quartile increased from 245.8% to 249.5% (p < .001). In hospitals in the top 90th percentile of total margin, every 10 min beyond the median ED boarding interval led to a decrease in total margin of 0.24%. PRACTICAL APPLICATIONS: Using the largest available national registry of ED operational data and concordant nonprofit financial reports, higher boarding among the highest-profitability hospitals (i.e., top 10%) is associated with a drag on profit margin, while hospitals with the highest boarding are associated with the highest leverage (i.e., indicated by the EM). These relationships suggest an association between a key ED indicator of hospital capacity management and overall institutional financial performance.

Dataset including whole blood gene expression profiles and matched leukocyte counts with utility for benchmarking cellular deconvolution pipelines.

OBJECTIVES: Cellular deconvolution is a valuable computational process that can infer the cellular composition of heterogeneous tissue samples from bulk RNA-sequencing data. Benchmark testing is a crucial step in the development and evaluation of new cellular deconvolution algorithms, and also plays a key role in the process of building and optimizing deconvolution pipelines for specific experimental applications. However, few in vivo benchmarking datasets exist, particularly for whole blood, which is the single most profiled human tissue. Here, we describe a unique dataset containing whole blood gene expression profiles and matched circulating leukocyte counts from a large cohort of human donors with utility for benchmarking cellular deconvolution pipelines. DATA DESCRIPTION: To produce this dataset, venous whole blood was sampled from 138 total donors recruited at an academic medical center. Genome-wide expression profiling was subsequently performed via next-generation RNA sequencing, and white blood cell differentials were collected in parallel using flow cytometry. The resultant final dataset contains donor-level expression data for over 45,000 protein coding and non-protein coding genes, as well as matched neutrophil, lymphocyte, monocyte, and eosinophil counts.

Assessing quality of hepato-pancreato-biliary surgery: nationwide benchmarking.

BACKGROUND: Clinical auditing is a powerful tool to evaluate and improve healthcare. Deviations from the expected quality of care are identified by benchmarking the results of individual hospitals using national averages. This study aimed to evaluate the use of quality indicators for benchmarking hepato-pancreato-biliary (HPB) surgery and when outlier hospitals could be identified. METHODS: A population-based study used data from two nationwide Dutch HPB audits (DHBA and DPCA) from 2014 to 2021. Sample size calculations determined the threshold (in percentage points) to identify centres as statistical outliers, based on current volume requirements (annual minimum of 20 resections) on a two-year period (2020-2021), covering mortality rate, failure to rescue (FTR), major morbidity rate and textbook/ideal outcome (TO) for minor liver resection (LR), major LR, pancreaticoduodenectomy (PD) and distal pancreatectomy (DP). RESULTS: In total, 10 963 and 7365 patients who underwent liver and pancreatic resection respectively were included. Benchmark and corresponding range of mortality rates were 0.6% (0 -3.2%) and 3.3% (0-16.7%) for minor and major LR, and 2.7% (0-7.0%) and 0.6% (0-4.2%) for PD and DP respectively. FTR rates were 5.4% (0-33.3%), 14.2% (0-100%), 7.5% (1.6%-28.5%) and 3.1% (0-14.9%). For major morbidity rate, corresponding rates were 9.8% (0-20.5%), 28.1% (0-47.1%), 36% (15.8%-58.3%) and 22.3% (5.2%-46.1%). For TO, corresponding rates were 73.6% (61.3%-94.4%), 54.1% (35.3-100), 46.8% (25.3%-59.4%) and 63.3% (30.7%-84.6%). Mortality rate thresholds indicating a significant outlier were 8.6% and 15.4% for minor and major LR and 14.2% and 8.6% for PD and DP. For FTR, these thresholds were 17.9%, 31.6%, 22.9% and 15.0%. For major morbidity rate, these thresholds were 26.1%, 49.7%, 57.9% and 52.9% respectively. For TO, lower thresholds were 52.5%, 32.5%, 25.8% and 41.4% respectively. Higher hospital volumes decrease thresholds to detect outliers. CONCLUSION: Current event rates and minimum volume requirements per hospital are too low to detect any meaningful between hospital differences in mortality rate and FTR. Major morbidity rate and TO are better candidates to use for benchmarking.

GRouNdGAN: GRN-guided simulation of single-cell RNA-seq data using causal generative adversarial networks.

We introduce GRouNdGAN, a gene regulatory network (GRN)-guided reference-based causal implicit generative model for simulating single-cell RNA-seq data, in silico perturbation experiments, and benchmarking GRN inference methods. Through the imposition of a user-defined GRN in its architecture, GRouNdGAN simulates steady-state and transient-state single-cell datasets where genes are causally expressed under the control of their regulating transcription factors (TFs). Training on six experimental reference datasets, we show that our model captures non-linear TF-gene dependencies and preserves gene identities, cell trajectories, pseudo-time ordering, and technical and biological noise, with no user manipulation and only implicit parameterization. GRouNdGAN can synthesize cells under new conditions to perform in silico TF knockout experiments. Benchmarking various GRN inference algorithms reveals that GRouNdGAN effectively bridges the existing gap between simulated and biological data benchmarks of GRN inference algorithms, providing gold standard ground truth GRNs and realistic cells corresponding to the biological system of interest.

Exploring memory synchronization and performance considerations for FPGA platform using the high-abstracted OpenCL framework: Benchmarks development and analysis.

A key benefit of the Open Computing Language (OpenCL) software framework is its capability to operate across diverse architectures. Field programmable gate arrays (FPGAs) are a high-speed computing architecture used for computation acceleration. This study investigates the impact of memory access time on overall performance in general FPGA computing environments through the creation of eight benchmarks within the OpenCL framework. The developed benchmarks capture a range of memory access behaviors, and they play a crucial role in assessing the performance of spinning and sleeping on FPGA-based architectures. The results obtained guide the formulation of new implementations and contribute to defining an abstraction of FPGAs. This abstraction is then utilized to create tailored implementations of primitives that are well-suited for this platform. While other research endeavors concentrate on creating benchmarks with the Compute Unified Device Architecture (CUDA) to scrutinize the memory systems across diverse GPU architectures and propose recommendations for future generations of GPU computation platforms, this study delves into the memory system analysis for the broader FPGA computing platform. It achieves this by employing the highly abstracted OpenCL framework, exploring various data workload characteristics, and experimentally delineating the appropriate implementation of primitives that can seamlessly integrate into a design tailored for the FPGA computing platform. Additionally, the results underscore the efficacy of employing a task-parallel model to mitigate the need for high-cost synchronization mechanisms in designs constructed on general FPGA computing platforms.

Benchmarking the university campus food environment and exploring student perspectives about food insecurity and healthy eating: a case study from Australia.

OBJECTIVE: To benchmark the university food environment and explore students' experiences with food insecurity and healthy eating in order to inform interventions to improve access and affordability of healthy foods for university students. DESIGN: A food environment audit was conducted on the university campus using the Uni-Food tool from April to May 2022 and was comprised of three main components, university systems and governance, campus facilities and environment, and food retail outlets. A qualitative study design was also used to conduct focus groups and semi-structured interviews with students to explore key themes regarding their experiences with food insecurity and healthy eating. SETTING: Macquarie University, Australia. PARTICIPANTS: For the food environment audit 24 retail outlets on campus and for the qualitative component 29 domestic and international students enrolled at Macquarie University. RESULTS: The university only scored 27% in total for all components in the food environment audit. The results showed the need for better governance and leadership of the food environment. The qualitative component suggested that the main barriers to accessing healthy foods were related to availability, pricing, and knowledge of healthy foods. Future intervention ideas included free fruits and vegetables, food relief, discounts, improved self-catering facilities, education, and increased healthy food outlets. CONCLUSIONS: Improving governance measures related to healthy eating on campus are a core priority to strengthen the food environment and students identified pricing and availability as key issues. These findings will inform effective and feasible interventions to improve food security and healthy eating on campus.

ORDerly: Data Sets and Benchmarks for Chemical Reaction Data.

Machine learning has the potential to provide tremendous value to life sciences by providing models that aid in the discovery of new molecules and reduce the time for new products to come to market. Chemical reactions play a significant role in these fields, but there is a lack of high-quality open-source chemical reaction data sets for training machine learning models. Herein, we present ORDerly, an open-source Python package for the customizable and reproducible preparation of reaction data stored in accordance with the increasingly popular Open Reaction Database (ORD) schema. We use ORDerly to clean United States patent data stored in ORD and generate data sets for forward prediction, retrosynthesis, as well as the first benchmark for reaction condition prediction. We train neural networks on data sets generated with ORDerly for condition prediction and show that data sets missing key cleaning steps can lead to silently overinflated performance metrics. Additionally, we train transformers for forward and retrosynthesis prediction and demonstrate how non-patent data can be used to evaluate model generalization. By providing a customizable open-source solution for cleaning and preparing large chemical reaction data, ORDerly is poised to push forward the boundaries of machine learning applications in chemistry.

Achieving optimal cord management: a multidisciplinary quality improvement initiative.

Optimal cord management (OCM), defined as waiting at least 60 seconds (s) before clamping the umbilical cord after birth, is an evidence-based intervention that improves outcomes for both term and preterm babies. All major resuscitation councils recommend OCM for well newborns.National Neonatal Audit Programme (NNAP) benchmarking data identified our tertiary neonatal unit as a negative outlier with regard to OCM practice with only 12.1% of infants receiving the recommended minimum of 60 s. This inspired a quality improvement project (QIP) to increase OCM rates of ≥ 60 s for infants <34 weeks. A multidisciplinary QIP team (Neonatal medical and nursing staff, Obstetricians, Midwives and Anaesthetic colleagues) was formed, and robust evidence-based quality improvement methodologies employed. Our aim was to increase OCM of ≥ 60 s for infants born at <34 weeks to at least 40%.The percentage of infants <34 weeks receiving OCM increased from 32.4% at baseline (June-September 2022) to 73.6% in the 9 months following QIP commencement (October 2022-June 2023). The intervention period spanned two cohorts of rotational doctors, demonstrating its sustainability. Rates of admission normothermia were maintained following the routine adoption of OCM (89.2% vs 88.5%), which is a complication described by other neonatal units.This project demonstrates the power of a multidisciplinary team approach to embedding an intervention that relies on collaboration between multiple departments. It also highlights the importance of national benchmarking data in allowing departments to focus QIP efforts to achieve long-lasting transformational service improvements.

A noise audit of human-labeled benchmarks for machine commonsense reasoning.

With the advent of large language models, evaluating and benchmarking these systems on important AI problems has taken on newfound importance. Such benchmarking typically involves comparing the predictions of a system against human labels (or a single 'ground-truth'). However, much recent work in psychology has suggested that most tasks involving significant human judgment can have non-trivial degrees of noise. In his book, Kahneman suggests that noise may be a much more significant component of inaccuracy compared to bias, which has been studied more extensively in the AI community. This article proposes a detailed noise audit of human-labeled benchmarks in machine commonsense reasoning, an important current area of AI research. We conduct noise audits under two important experimental conditions: one in a smaller-scale but higher-quality labeling setting, and another in a larger-scale, more realistic online crowdsourced setting. Using Kahneman's framework of noise, our results consistently show non-trivial amounts of level, pattern, and system noise, even in the higher-quality setting, with comparable results in the crowdsourced setting. We find that noise can significantly influence the performance estimates that we obtain of commonsense reasoning systems, even if the 'system' is a human; in some cases, by almost 10 percent. Labeling noise also affects performance estimates of systems like ChatGPT by more than 4 percent. Our results suggest that the default practice in the AI community of assuming and using a 'single' ground-truth, even on problems requiring seemingly straightforward human judgment, may warrant empirical and methodological re-visiting.

Usability of an Automated System for Real-Time Monitoring of Shared Decision-Making for Surgery: Mixed Methods Evaluation.

BACKGROUND: Improving shared decision-making (SDM) for patients has become a health policy priority in many countries. Achieving high-quality SDM is particularly important for approximately 313 million surgical treatment decisions patients make globally every year. Large-scale monitoring of surgical patients' experience of SDM in real time is needed to identify the failings of SDM before surgery is performed. We developed a novel approach to automating real-time data collection using an electronic measurement system to address this. Examining usability will facilitate its optimization and wider implementation to inform interventions aimed at improving SDM. OBJECTIVE: This study examined the usability of an electronic real-time measurement system to monitor surgical patients' experience of SDM. We aimed to evaluate the metrics and indicators relevant to system effectiveness, system efficiency, and user satisfaction. METHODS: We performed a mixed methods usability evaluation using multiple participant cohorts. The measurement system was implemented in a large UK hospital to measure patients' experience of SDM electronically before surgery using 2 validated measures (CollaboRATE and SDM-Q-9). Quantitative data (collected between April 1 and December 31, 2021) provided measurement system metrics to assess system effectiveness and efficiency. We included adult patients booked for urgent and elective surgery across 7 specialties and excluded patients without the capacity to consent for medical procedures, those without access to an internet-enabled device, and those undergoing emergency or endoscopic procedures. Additional groups of service users (group 1: public members who had not engaged with the system; group 2: a subset of patients who completed the measurement system) completed user-testing sessions and semistructured interviews to assess system effectiveness and user satisfaction. We conducted quantitative data analysis using descriptive statistics and calculated the task completion rate and survey response rate (system effectiveness) as well as the task completion time, task efficiency, and relative efficiency (system efficiency). Qualitative thematic analysis identified indicators of and barriers to good usability (user satisfaction). RESULTS: A total of 2254 completed surveys were returned to the measurement system. A total of 25 service users (group 1: n=9; group 2: n=16) participated in user-testing sessions and interviews. The task completion rate was high (169/171, 98.8%) and the survey response rate was good (2254/5794, 38.9%). The median task completion time was 3 (IQR 2-13) minutes, suggesting good system efficiency and effectiveness. The qualitative findings emphasized good user satisfaction. The identified themes suggested that the measurement system is acceptable, easy to use, and easy to access. Service users identified potential barriers and solutions to acceptability and ease of access. CONCLUSIONS: A mixed methods evaluation of an electronic measurement system for automated, real-time monitoring of patients' experience of SDM showed that usability among patients was high. Future pilot work will optimize the system for wider implementation to ultimately inform intervention development to improve SDM. INTERNATIONAL REGISTERED REPORT IDENTIFIER (IRRID): RR2-10.1136/bmjopen-2023-079155.

Transitioning to adulthood: Are conventional benchmarks as protective today as they were in the past?

More young adults in the United States are studying beyond high school and working full-time than in the past, yet young adults continue to have high poverty rates as they transition to adulthood. This study uses longitudinal data on two cohorts of young adults from the 1979 and 1997 National Longitudinal Study of Youth to assess whether conventional benchmarks associated with economic success-gaining an education, finding stable employment, and delaying childbirth until after marriage-are as predictive of reduced poverty today as they were in the past. We also explore differences in the protective effect of the benchmarks by race/ethnicity, gender, and poverty status while young. We find that, on average, the benchmarks associated with economic success are as predictive of reduced poverty among young adults today as they were for the prior generation; however, demographics and features of the economy have contributed to higher poverty rates among today's young adults.

Cataract-1K Dataset for Deep-Learning-Assisted Analysis of Cataract Surgery Videos.

In recent years, the landscape of computer-assisted interventions and post-operative surgical video analysis has been dramatically reshaped by deep-learning techniques, resulting in significant advancements in surgeons' skills, operation room management, and overall surgical outcomes. However, the progression of deep-learning-powered surgical technologies is profoundly reliant on large-scale datasets and annotations. In particular, surgical scene understanding and phase recognition stand as pivotal pillars within the realm of computer-assisted surgery and post-operative assessment of cataract surgery videos. In this context, we present the largest cataract surgery video dataset that addresses diverse requisites for constructing computerized surgical workflow analysis and detecting post-operative irregularities in cataract surgery. We validate the quality of annotations by benchmarking the performance of several state-of-the-art neural network architectures for phase recognition and surgical scene segmentation. Besides, we initiate the research on domain adaptation for instrument segmentation in cataract surgery by evaluating cross-domain instrument segmentation performance in cataract surgery videos. The dataset and annotations are publicly available in Synapse.

MultiToxPred 1.0: a novel comprehensive tool for predicting 27 classes of protein toxins using an ensemble machine learning approach.

Protein toxins are defense mechanisms and adaptations found in various organisms and microorganisms, and their use in scientific research as therapeutic candidates is gaining relevance due to their effectiveness and specificity against cellular targets. However, discovering these toxins is time-consuming and expensive. In silico tools, particularly those based on machine learning and deep learning, have emerged as valuable resources to address this challenge. Existing tools primarily focus on binary classification, determining whether a protein is a toxin or not, and occasionally identifying specific types of toxins. For the first time, we propose a novel approach capable of classifying protein toxins into 27 distinct categories based on their mode of action within cells. To accomplish this, we assessed multiple machine learning techniques and found that an ensemble model incorporating the Light Gradient Boosting Machine and Quadratic Discriminant Analysis algorithms exhibited the best performance. During the tenfold cross-validation on the training dataset, our model exhibited notable metrics: 0.840 accuracy, 0.827 F1 score, 0.836 precision, 0.840 sensitivity, and 0.989 AUC. In the testing stage, using an independent dataset, the model achieved 0.846 accuracy, 0.838 F1 score, 0.847 precision, 0.849 sensitivity, and 0.991 AUC. These results present a powerful next-generation tool called MultiToxPred 1.0, accessible through a web application. We believe that MultiToxPred 1.0 has the potential to become an indispensable resource for researchers, facilitating the efficient identification of protein toxins. By leveraging this tool, scientists can accelerate their search for these toxins and advance their understanding of their therapeutic potential.

Heart Rate Variability and Pulse Rate Variability: Do Anatomical Location and Sampling Rate Matter?

Wearable technology and neuroimaging equipment using photoplethysmography (PPG) have become increasingly popularized in recent years. Several investigations deriving pulse rate variability (PRV) from PPG have demonstrated that a slight bias exists compared to concurrent heart rate variability (HRV) estimates. PPG devices commonly sample at ~20-100 Hz, where the minimum sampling frequency to derive valid PRV metrics is unknown. Further, due to different autonomic innervation, it is unknown if PRV metrics are harmonious between the cerebral and peripheral vasculature. Cardiac activity via electrocardiography (ECG) and PPG were obtained concurrently in 54 participants (29 females) in an upright orthostatic position. PPG data were collected at three anatomical locations: left third phalanx, middle cerebral artery, and posterior cerebral artery using a Finapres NOVA device and transcranial Doppler ultrasound. Data were sampled for five minutes at 1000 Hz and downsampled to frequencies ranging from 20 to 500 Hz. HRV (via ECG) and PRV (via PPG) were quantified and compared at 1000 Hz using Bland-Altman plots and coefficient of variation (CoV). A sampling frequency of ~100-200 Hz was required to produce PRV metrics with a bias of less than 2%, while a sampling rate of ~40-50 Hz elicited a bias smaller than 20%. At 1000 Hz, time- and frequency-domain PRV measures were slightly elevated compared to those derived from HRV (mean bias: ~1-8%). In conjunction with previous reports, PRV and HRV were not surrogate biomarkers due to the different nature of the collected waveforms. Nevertheless, PRV estimates displayed greater validity at a lower sampling rate compared to HRV estimates.

Fundamental and Practical Feasibility of Electrocardiogram Reconstruction from Photoplethysmogram.

Electrocardiogram (ECG) reconstruction from contact photoplethysmogram (PPG) would be transformative for cardiac monitoring. We investigated the fundamental and practical feasibility of such reconstruction by first replicating pioneering work in the field, with the aim of assessing the methods and evaluation metrics used. We then expanded existing research by investigating different cycle segmentation methods and different evaluation scenarios to robustly verify both fundamental feasibility, as well as practical potential. We found that reconstruction using the discrete cosine transform (DCT) and a linear ridge regression model shows good results when PPG and ECG cycles are semantically aligned-the ECG R peak and PPG systolic peak are aligned-before training the model. Such reconstruction can be useful from a morphological perspective, but loses important physiological information (precise R peak location) due to cycle alignment. We also found better performance when personalization was used in training, while a general model in a leave-one-subject-out evaluation performed poorly, showing that a general mapping between PPG and ECG is difficult to derive. While such reconstruction is valuable, as the ECG contains more fine-grained information about the cardiac activity as well as offers a different modality (electrical signal) compared to the PPG (optical signal), our findings show that the usefulness of such reconstruction depends on the application, with a trade-off between morphological quality of QRS complexes and precise temporal placement of the R peak. Finally, we highlight future directions that may resolve existing problems and allow for reliable and robust cross-modal physiological monitoring using just PPG.

Smartphone-Derived Seismocardiography: Robust Approach for Accurate Cardiac Energy Assessment in Patients with Various Cardiovascular Conditions.

Seismocardiography (SCG), a method for measuring heart-induced chest vibrations, is gaining attention as a non-invasive, accessible, and cost-effective approach for cardiac pathologies, diagnosis, and monitoring. This study explores the integration of SCG acquired through smartphone technology by assessing the accuracy of metrics derived from smartphone recordings and their consistency when performed by patients. Therefore, we assessed smartphone-derived SCG's reliability in computing median kinetic energy parameters per record in 220 patients with various cardiovascular conditions. The study involved three key procedures: (1) simultaneous measurements of a validated hardware device and a commercial smartphone; (2) consecutive smartphone recordings performed by both clinicians and patients; (3) patients' self-conducted home recordings over three months. Our findings indicate a moderate-to-high reliability of smartphone-acquired SCG metrics compared to those obtained from a validated device, with intraclass correlation (ICC) > 0.77. The reliability of patient-acquired SCG metrics was high (ICC > 0.83). Within the cohort, 138 patients had smartphones that met the compatibility criteria for the study, with an observed at-home compliance rate of 41.4%. This research validates the potential of smartphone-derived SCG acquisition in providing repeatable SCG metrics in telemedicine, thus laying a foundation for future studies to enhance the precision of at-home cardiac data acquisition.

Triple Generative Self-Supervised Learning Method for Molecular Property Prediction.

Molecular property prediction is an important task in drug discovery, and with help of self-supervised learning methods, the performance of molecular property prediction could be improved by utilizing large-scale unlabeled dataset. In this paper, we propose a triple generative self-supervised learning method for molecular property prediction, called TGSS. Three encoders including a bi-directional long short-term memory recurrent neural network (BiLSTM), a Transformer, and a graph attention network (GAT) are used in pre-training the model using molecular sequence and graph structure data to extract molecular features. The variational auto encoder (VAE) is used for reconstructing features from the three models. In the downstream task, in order to balance the information between different molecular features, a feature fusion module is added to assign different weights to each feature. In addition, to improve the interpretability of the model, atomic similarity heat maps were introduced to demonstrate the effectiveness and rationality of molecular feature extraction. We demonstrate the accuracy of the proposed method on chemical and biological benchmark datasets by comparative experiments.