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The design of heterogeneous catalysts generally involves optimizing the reactivity descriptor of adsorption energy, which is inevitably governed by the structure of surface-active sites. A prerequisite for understanding the structure–properties relationship is the precise identification of real surface-active site structures, rather than relying on conceived structures derived from bulk alloy properties. However, it remains a formidable challenge due to the dynamic nature of nanoalloys during catalytic reactions and the lack of accurate and efficient interatomic potentials for simulations. Herein, a generalizable deep-learning potential for the Ag–Pd–F system is developed based on a dataset encompassing the bulk, surface, nanocluster, amorphous, and point defected configurations with diverse compositions to achieve a comprehensive description of interatomic interactions, facilitating precise prediction of adsorption energy, surface energy, formation energy, and diffusion energy barrier and is utilized to investigate the structural evolutions of AgPd nanoalloys during fluorination. The structural evolutions involve the inward diffusion of F, the outward diffusion of Ag in Ag@Pd nanoalloys, the formation of surface AgFx species in mixed and Janus AgPd nanoalloys, and the shape deformation from cuboctahedron to sphere in Ag and Pd@Ag nanoalloys. Moreover, the effects of atomic diffusion and dislocation formation and migration on the reconstructing pathway of nanoalloys are highlighted. It is demonstrated that the stress relaxation upon F adsorption serves as the intrinsic driving factor governing the surface reconstruction of AgPd nanoalloys. [ABSTRACT FROM AUTHOR]

The present work shows that the free energy landscape associated with alanine dipeptide isomerization can be effectively represented by specific interatomic distances without explicit reference to dihedral angles. Conventionally, two stable states of alanine dipeptide in vacuum, i.e., C7eq (β-sheet structure) and C7ax (left handed α-helix structure), have been primarily characterized using the main chain dihedral angles, φ (C–N–Cα–C) and ψ (N–Cα–C–N). However, our recent deep learning combined with the "Explainable AI" (XAI) framework has shown that the transition state can be adequately captured by a free energy landscape using φ and θ (O–C–N–Cα) [Kikutsuji et al., J. Chem. Phys. 156, 154108 (2022)]. In the perspective of extending these insights to other collective variables, a more detailed characterization of the transition state is required. In this work, we employ interatomic distances and bond angles as input variables for deep learning rather than the conventional and more elaborate dihedral angles. Our approach utilizes deep learning to investigate whether changes in the main chain dihedral angle can be expressed in terms of interatomic distances and bond angles. Furthermore, by incorporating XAI into our predictive analysis, we quantified the importance of each input variable and succeeded in clarifying the specific interatomic distance that affects the transition state. The results indicate that constructing a free energy landscape based on the identified interatomic distance can clearly distinguish between the two stable states and provide a comprehensive explanation for the energy barrier crossing. [ABSTRACT FROM AUTHOR]

Several enhanced sampling techniques rely on the definition of collective variables to effectively explore free energy landscapes. The existing variables that describe the progression along a reactive pathway offer an elegant solution but face a number of limitations. In this paper, we address these challenges by introducing a new path-like collective variable called the "deep-locally non-linear-embedding," which is inspired by principles of the locally linear embedding technique and is trained on a reactive trajectory. The variable mimics the ideal reaction coordinate by automatically generating a non-linear combination of features through a differentiable generalized autoencoder that combines a neural network with a continuous k-nearest neighbor selection. Among the key advantages of this method is its capability to automatically choose the metric for searching neighbors and to learn the path from state A to state B without the need to handpick landmarks a priori. We demonstrate the effectiveness of DeepLNE by showing that the progression along the path variable closely approximates the ideal reaction coordinate in toy models, such as the Müller-Brown potential and alanine dipeptide. Then, we use it in the molecular dynamics simulations of an RNA tetraloop, where we highlight its capability to accelerate transitions and estimate the free energy of folding. [ABSTRACT FROM AUTHOR]

Metal organic frameworks (MOFs) are crystalline, three-dimensional structures with high surface areas and tunable porosities. Made from metal nodes connected by organic linkers, the exact properties of a given MOF are determined by node and linker choice. MOFs hold promise for numerous applications, including gas capture and storage. M2(4,4′-dioxidobiphenyl-3,3′-dicarboxylate)—henceforth simply M2(dobpdc), with M = Mg, Mn, Fe, Co, Ni, Cu, or Zn—is regarded as one of the most promising structures for CO2 capture applications. Further modification of the MOF with diamines or tetramines can significantly boost gas species selectivity, a necessity for the ultra-dilute CO2 concentrations in the direct-air capture of CO2. There are countless potential diamines and tetramines, paving the way for a vast number of potential sorbents to be probed for CO2 adsorption properties. The number of amines and their configuration in the MOF pore are key drivers of CO2 adsorption capacity and kinetics, and so a validation of computational prediction of these quantities is required to suitably use computational methods in the discovery and screening of amine-functionalized sorbents. In this work, we study the predictive accuracy of density functional theory and related calculations on amine loading and configuration for one diamine and two tetramines. In particular, we explore the Perdew–Burke–Ernzerhof (PBE) functional and its formulation for solids (PBEsol) with and without the Grimme-D2 and Grimme-D3 pairwise corrections (PBE+D2/3 and PBEsol+D2/3), two revised PBE functionals with the Grimme-D2 and Grimme-D3 pairwise corrections (RPBE+D2/3 and revPBE+D2/3), and the nonlocal van der Waals correlation (vdW-DF2) functional. We also investigate a universal graph deep learning interatomic potential's (M3GNet) predictive accuracy for loading and configuration. These results allow us to identify a useful screening procedure for configuration prediction that has a coarse component for quick evaluation and a higher accuracy component for detailed analysis. Our general observation is that the neural network-based potential can be used as a high-level and rapid screening tool, whereas PBEsol+D3 gives a completely qualitatively predictive picture across all systems studied, and can thus be used for high accuracy motif predictions. We close by briefly exploring the predictions of relative thermal stability for the different functionals and dispersion corrections. [ABSTRACT FROM AUTHOR]

The current focus in Autonomous Experimentation (AE) is on developing robust workflows to conduct the AE effectively. This entails the need for well-defined approaches to guide the AE process, including strategies for hyperparameter tuning and high-level human interventions within the workflow loop. This paper presents a comprehensive analysis of the influence of initial experimental conditions and in-loop interventions on the learning dynamics of Deep Kernel Learning (DKL) within the realm of AE in scanning probe microscopy. We explore the concept of the "seed effect," where the initial experiment setup has a substantial impact on the subsequent learning trajectory. Additionally, we introduce an approach of the seed point interventions in AE allowing the operator to influence the exploration process. Using a dataset from Piezoresponse Force Microscopy on PbTiO3 thin films, we illustrate the impact of the "seed effect" and in-loop seed interventions on the effectiveness of DKL in predicting material properties. The study highlights the importance of initial choices and adaptive interventions in optimizing learning rates and enhancing the efficiency of automated material characterization. This work offers valuable insights into designing more robust and effective AE workflows in microscopy with potential applications across various characterization techniques. [ABSTRACT FROM AUTHOR]

In this research, we utilized density functional theory (DFT) computations to perform ab initio molecular dynamics simulations and static calculations on graphene, hexagonal boron nitride, and their heterostructures, subjecting them to strains, perturbations, twist angles, and defects. The gathered energy, force, and virial information informed the creation of a training set comprising 1253 structures. Employing the Neural Evolutionary Potential framework integrated into Graphics Processing Units Molecular Dynamics, we fitted a machine learning potential (MLP) that closely mirrored the DFT potential energy surface. Rigorous validation of lattice constants and phonon dispersion relations confirmed the precision and dependability of the MLP, establishing a solid foundation for subsequent thermal transport investigations. A further analysis of the impact of twist angles uncovered a significant reduction in thermal conductivity, particularly notable in heterostructures with a decline exceeding 35%. The reduction in thermal conductivity primarily stems from the twist angle-induced softening of phonon modes and the accompanying increase in phonon scattering rates, which intensifies anharmonic interactions among phonons. Our study underscores the efficacy of the MLP in delineating the thermal transport attributes of two-dimensional materials and their heterostructures, while also elucidating the micro-mechanisms behind the influence of the twist angle on thermal conductivity, offering fresh perspectives for the design of advanced thermal management materials. [ABSTRACT FROM AUTHOR]

Pump–probe thermoreflectance has been commonly applied for characterizing the thermal properties of materials. Generally, a reliable and efficient non-linear fitting process is often implemented to extract unknown thermal parameters during the pump–probe thermoreflectance characterizations. However, when it comes to processing large amounts of data acquired from similar structural samples, non-linear fitting process appears to be very time-consuming and labor-intensive to search for the best fitting for every testing curve. Herein, we propose to apply deep learning (DL) approach to nanosecond transient thermoreflectance technique for high-throughput experimental data processing. We first investigated the effect of training set parameters (density and bounds) on the predictive performance of the DL model, providing a guidance to optimize the DL model. Then, the DL model is further verified in the measurement of the bulk sapphire, SiC, diamond samples, and GaN-based multilayer structures, demonstrating its capability of analyzing the results with high accuracy. Compared to the conventional non-linear fitting method (such as Global Optimization), the computation time of the new model is 1000 times lower. Such a data-driven DL model enables the faster inference and stronger fitting capabilities and is particularly efficient and effective in processing data acquired from wafer-level measurements with similar material structures. [ABSTRACT FROM AUTHOR]

Online ride-hailing services provide additional transportation capability by recruiting private vehicles to meet people's growing travel demand. To ensure the profitability of drivers and platforms, pick-up efficiency and frequency must be maintained at high levels. Therefore, consistency between the spatial distribution of drivers and that of travel demand becomes a key issue to address. This paper proposes a prediction-based iterative Kuhn-Munkres approach for service vehicle reallocation in the context of large-scale online ride-hailing. Firstly, preliminaries are formally defined and a novel mathematical model for the problem is proposed. Secondly, a deep spatio-temporal residual perception network is designed to accurately predict travel demand. Thirdly, an iterative Kuhn-Munkres approach combined with an improved A-Star algorithm is developed to reallocate service vehicles to spatial locations according to their distinct travel demand densities. Finally, extensive experiments are conducted to evaluate and verify the performance of the proposed approach. [ABSTRACT FROM AUTHOR]

GoogLeNet is a pre-trained Convolutional Neural Network (CNN) that allows transfer learning and has achieved high recognition rates in image classification tasks. A Recurrence Plot (RP) is an imaging method that depicts the recurrence of the state space system using coloured points and lines in 2D images. This work contributes to facilitating time series feature extraction by proposing a method that applies the GoogLeNet to time series images obtained with RP. The developed method is tested using simulated time series and selected time series from the M3 competition dataset. The results shows that the transfer learning approach allowed the extraction of business time series features by means of a GoogLeNet fine-tuned using 100 simulated time series. The combination of GoogLeNet and RPs outperforms the alternative and easier combination of GoogLeNet and plots of the time series and support the convenience of the RP transformation step. This application of deep learning techniques to business time series imaging offers opportunity for further developments. [ABSTRACT FROM AUTHOR]

In nowadays production, fluctuations in demand, shortening product life-cycles, and highly configurable products require an adaptive and robust control approach to maintain competitiveness. This approach must not only optimise desired production objectives but also cope with unforeseen machine failures, rush orders, and changes in short-term demand. Previous control approaches were often implemented using a single operations layer and a standalone deep learning approach, which may not adequately address the complex organisational demands of modern manufacturing systems. To address this challenge, we propose a hyper-heuristics control model within a semi-heterarchical production system, in which multiple manufacturing and distribution agents are spread across pre-defined modules. The agents employ a deep reinforcement learning algorithm to learn a policy for selecting low-level heuristics in a situation-specific manner, thereby leveraging system performance and adaptability. We tested our approach in simulation and transferred it to a hybrid production environment. By that, we were able to demonstrate its multi-objective optimisation capabilities compared to conventional approaches in terms of mean throughput time, tardiness, and processing of prioritised orders in a multi-layered production system. The modular design is promising in reducing the overall system complexity and facilitates a quick and seamless integration into other scenarios. [ABSTRACT FROM AUTHOR]

The inventory levels of pickup points play an important role for the same-day or next-day pickup and delivery services. The previous inventory optimisation research usually makes an assumption about demand distribution, does not use the real dataset or consider shipping strategies for this problem. In this study, we introduce a new strategy, mixture of anticipatory and emergency shipping, and propose forecasting-optimisation integrated approach to optimise multi-items' inventories in each pickup point based on big data analysis. We explore a real dataset including 23,808,261 records with 54 pickup points and 4018 items. We first cluster the dataset based on the distances between pickup points and the warehouse, then, implement the forecasting-optimisation integrated algorithms to select the more profitable strategy for each group. The result indicates that compared with the original algorithms, our proposed approach can effectively increase the profits, particularly, the novel algorithm, Long Short-Term Memory networks – Quantile Regression, performs better. Additionally, we find that the 100% anticipatory shipping is not necessarily superior to emergency shipment, when the pickup point is farther from the warehouse, the advantage of emergency shipment is more significant. However, the mixture of anticipatory and emergency shipping can contribute to higher profits for online retailers. [ABSTRACT FROM AUTHOR]

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The rapid proliferation of complex information systems has been met by an ever-increasing quantity of exploits that can cause irreparable cyber breaches. To mitigate these cyber threats, academia and industry have placed a significant focus on proactively identifying and labeling exploits developed by the international hacker community. However, prevailing approaches for labeling exploits in hacker forums do not leverage metadata from exploit darknet markets or public exploit repositories to enhance labeling performance. In this study, we adopted the computational design science paradigm to develop a novel information technology artifact, the deep transfer learning exploit labeler (DTL-EL). DTL-EL incorporates a pre-initialization design, multi-layer deep transfer learning (DTL), and a self-attention mechanism to automatically label exploits in hacker forums. We rigorously evaluated the proposed DTL-EL against state-of-the-art non-DTL benchmark methods based in classical machine learning and deep learning. Results suggest that the proposed DTL-EL significantly outperforms benchmark methods based on accuracy, precision, recall, and F1-score. Our proposed DTL-EL framework provides important practical implications for key stakeholders such as cybersecurity managers, analysts, and educators. [ABSTRACT FROM AUTHOR]

Automatic determination of manufacturing process sequences for the physical production of given part designs is key to facilitate on-demand cyber manufacturing. In this work, we propose an integrated framework that (i) identifies manufacturing features from 3D part designs using a Graph Neural Network (GNN), (ii) identifies the manufacturing processes necessary to produce all features in the part using a Convolutional Neural Network (CNN) that considers shape, material properties, and quality information, and (iii) outputs an ordered manufacturing sequence that can produce the designed part with the help of sequence mining. Using these methods, the knowledge required to enable automated manufacturing process selection is easily scalable and updatable without requiring manual population of ad-hoc or rule-based descriptions. We present exemplar implementations of the proposed framework by suggesting manufacturing sequences for discrete parts with multiple features. The suggested manufacturing sequences demonstrate the potential of the proposed framework for use in future on-demand cyber manufacturing applications. [ABSTRACT FROM AUTHOR]

This paper considers two pertinent research inquiries: 'Can an AI-based predictive framework be utilised for the optimisation of solar energy management?' and 'What are the ways in which the AI-based predictive framework can be integrated within the Smart Grid infrastructure to improve grid reliability and efficiency?' The study deploys a Deep Learning model based on Long Short-Term Memory techniques, leading to refined accuracy in solar electricity generation forecasts. Such an AI-supported methodology aids power grid operators in comprehensive planning, thereby ensuring a robust electricity supply. The effectiveness of this framework is tested using performance metrics such as MAE, RMSE, nMAE, nRMSE, and $ R^2 $ R 2 . A persistent model is utilised as a reference for comparison. Despite a slight decrease in predictive precision with the expansion of the forecast horizon, the proposed AI-based framework consistently surpasses the persistent model, particularly for horizons beyond two hours. Therefore, this research underscores the potential of AI-based prediction in fostering efficient solar energy management and enhancing Smart Grid reliability and efficiency. [ABSTRACT FROM AUTHOR]

Influencer marketing, in which companies sponsor social media personalities to promote their brands, has exploded in popularity in recent years. One common criterion for selecting an influencer partner is popularity. While some firms collaborate with "mega" influencers with millions of followers, other firms partner with "micro" influencers with only several thousand followers, but who also cost less to sponsor. To quantify this trade-off between popularity and cost, the authors develop a framework for estimating the follower elasticity of impressions (FEI), which measures a video's percentage gain in impressions (i.e., views) corresponding to a percentage increase in the number of followers of its creator. Computing FEI involves estimating the causal effect of an influencer's popularity on the view counts of their videos, which is achieved through a combination of (1) a unique data set collected from TikTok, (2) a representation learning model for quantifying video content, and (3) a machine learning–based causal inference method. The authors find that FEI is always positive, averaging.10, but often nonlinearly related to follower size. They examine the factors that predict variation in these FEI curves and show how firms can use these results to better determine influencer partnerships. [ABSTRACT FROM AUTHOR]

Background and purposeMotion management is essential to reduce normal tissue exposure and maintain adequate tumor dose in lung stereotactic body radiation therapy (SBRT). Lung SBRT using an articulated robotic arm allows dynamic tracking during radiation dose delivery. Two stereoscopic X-ray tracking modes are available - fiducial-based and fiducial-free tracking. Although X-ray detection of implanted fiducials is robust, the implantation procedure is invasive and inapplicable to some patients and tumor locations. Fiducial-free tracking relies on tumor contrast, which challenges the existing tracking algorithms for small (e.g., 15 mm) and tumor locations (with/without thoracic anatomy overlapping).ResultsOn X-ray views that conventional methods failed to track the lung tumor, Deep Match achieved robust performance as evidenced by >80 % 3 mm-Hit (detection within 3 mm superior/inferior margin from ground truth) for 70 % of patients and

DLSIA (Deep Learning for Scientific Image Analysis) is a Python-based machine learning library that empowers scientists and researchers across diverse scientific domains with a range of customizable convolutional neural network (CNN) architectures for a wide variety of tasks in image analysis to be used in downstream data processing. DLSIA features easy-to-use architectures, such as autoencoders, tunable U-Nets and parameter-lean mixed-scale dense networks (MSDNets). Additionally, this article introduces sparse mixed-scale networks (SMSNets), generated using random graphs, sparse connections and dilated convolutions connecting different length scales. For verification, several DLSIA-instantiated networks and training scripts are employed in multiple applications, including inpainting for X-ray scattering data using U-Nets and MSDNets, segmenting 3D fibers in X-ray tomographic reconstructions of concrete using an ensemble of SMSNets, and leveraging autoencoder latent spaces for data compression and clustering. As experimental data continue to grow in scale and complexity, DLSIA provides accessible CNN construction and abstracts CNN complexities, allowing scientists to tailor their machine learning approaches, accelerate discoveries, foster interdisciplinary collaboration and advance research in scientific image analysis.

Many machine learning techniques are used as drug discovery tools with the intent to speed characterization by determining relationships between compound structure and biological function. However, particularly in anticancer drug discovery, these models often make only binary decisions about the biological activity for a narrow scope of drug targets. We present a feed-forward neural network, PECAN (Prediction Engine for the Cytostatic Activity of Natural product-like compounds), that simultaneously classifies the potential antiproliferative activity of compounds against 59 cancer cell lines. It predicts the activity to be one of six categories, indicating not only if activity is present but the degree of activity. Using an independent subset of NCI data as a test set, we show that PECAN can reach 60.1% accuracy in a six-way classification and present further evidence that it classifies based on useful structural features of compounds using a within-one measure that reaches 93.0% accuracy.

As the field of computational cognitive neuroscience continues to expand and generate new theories, there is a growing need for more advanced methods to test the hypothesis of brain-behavior relationships. Recent progress in Bayesian cognitive modeling has enabled the combination of neural and behavioral models into a single unifying framework. However, these approaches require manual feature extraction, and lack the capability to discover previously unknown neural features in more complex data. Consequently, this would hinder the expressiveness of the models. To address these challenges, we propose a Neurocognitive Variational Autoencoder (NCVA) to conjoin high-dimensional EEG with a cognitive model in both generative and predictive modeling analyses. Importantly, our NCVA enables both the prediction of EEG signals given behavioral data and the estimation of cognitive model parameters from EEG signals. This novel approach can allow for a more comprehensive understanding of the triplet relationship between behavior, brain activity, and cognitive processes.

The evaluation of thermoelectric materials relies significantly on the thermoelectric figure of merit, ZT, which serves as a crucial parameter in assessing their properties. The accurate prediction of ZT values can be accomplished by utilizing machine learning models to learn material characteristics. However, factors such as the size of the dataset, model hyperparameters, and data quality can all impact the accuracy of machine learning. In contrast to previous research where high-dimensional features were simply discarded to transform them into low-dimensional ones, deep learning models such as autoencoder can extract more effective information. Therefore, in this article, the combination of autoencoders and the Light Gradient Boosting Machine (LightGBM) is employed to learn the chemical characteristics and ZT values of various materials. The reliability of the model was confirmed by achieving an R2 score of 0.94 during tenfold cross-validation. 130 000 materials were predicted and screened, the temperature dependence of the screened materials was studied in depth, and 13 materials with high ZT values were identified. Four of the 13 most promising candidates identified are existing thermoelectric materials, while nine are ideal candidates for future experimental studies and validation. This work utilizes autoencoders for extensive prediction and screening of promising materials, providing an effective approach for handling high-dimensional material data. [ABSTRACT FROM AUTHOR]

Disordered molecular systems, such as amorphous catalysts, organic thin films, electrolyte solutions, and water, are at the cutting edge of computational exploration at present. Traditional simulations of such systems at length scales relevant to experiments in practice require a compromise between model accuracy and quality of sampling. To address this problem, we have developed an approach based on generative machine learning called the Morphological Autoregressive Protocol (MAP), which provides computational access to mesoscale disordered molecular configurations at linear cost at generation for materials in which structural correlations decay sufficiently rapidly. The algorithm is implemented using an augmented PixelCNN deep learning architecture that, as we previously demonstrated, produces excellent results in 2 dimensions (2D) for mono-elemental molecular systems. Here, we extend our implementation to multi-elemental 3D and demonstrate performance using water as our test system in two scenarios: (1) liquid water and (2) samples conditioned on the presence of pre-selected motifs. We trained the model on small-scale samples of liquid water produced using path-integral molecular dynamics simulations, including nuclear quantum effects under ambient conditions. MAP-generated water configurations are shown to accurately reproduce the properties of the training set and to produce stable trajectories when used as initial conditions in quantum dynamics simulations. We expect our approach to perform equally well on other disordered molecular systems in which structural correlations decay sufficiently fast while offering unique advantages in situations when the disorder is quenched rather than equilibrated. [ABSTRACT FROM AUTHOR]

Acoustic holography (AH) provides a promising technique for arbitrary acoustic field reconstruction, supporting many applications like robotic micro-nano manipulation, neuromodulation, volumetric imaging, and virtual reality. In AH, three-dimensional (3D) acoustic fields quantified with complex-valued acoustic pressures are reconstructed by virtue of two-dimensional (2D) acoustic holograms. Phase-only hologram (POH) is recently regarded as an energy-efficient way for AH, which is typically implemented by a dynamically programmable phased array of transducers (PATs). As a result, spatiotemporal precise acoustic field reconstruction is enabled by precise, dynamic, and individual actuation of PAT. Thus, 2D POH is required per arbitrary acoustic fields, which can be viewed as a physical inverse problem. However, solving the aforementioned physical inverse problem in numerical manners poses challenges due to its non-linear, high-dimensional, and complex coupling natures. The existing iterative algorithms like the iterative angular spectrum approach (IASA) and iterative backpropagation (IB) still suffer from speed-accuracy trade-offs. Hence, this paper explores a novel physics-iterative-reinforced deep learning method, in which frequency-argument contrastive learning is proposed facilitated by the inherent physical nature of AH, and the energy conservation law is under consideration. The experimental results demonstrate the effectiveness of the proposed method for acoustic field reconstruction, highlighting its significant potential in the domain of acoustics, and pushing forward the combination of physics into deep learning. [ABSTRACT FROM AUTHOR]

In modern large-scale industrial processes, data are often high dimensional time-dependent due to the frequent sampling, dynamic nature and large number of variables. Appropriate monitoring of such processes allows for efficient decision-making that can improve the baseline of manufacturing companies either through decreasing production costs or enhancing production efficiency. Various latent variable-based control charts have been proposed for addressing high dimensional data; however, many of these methods assume that the data are independent and normally distributed. The violation of these assumptions results in an increased false alarm rate, in addition to the deterioration in the performance of such methods. In this study, we propose a Variational Autoencoder-Long Short Term Memory (VAE-LSTM) deep learning based $ {T^2} $ T 2 chart that integrates the unique features of both VAE and LSTM for intelligent fault detection of time-dependent high dimensional processes. The effectiveness and applicability of the proposed model are demonstrated through extensive simulations, an open-source online dataset, and a real case study. [ABSTRACT FROM AUTHOR]

Designing an incentive compatible auction that maximizes expected revenue is an intricate task. The single-item case was resolved in a seminal piece of work by Myerson in 1981, but more than 40 years later, a full analytical understanding of the optimal design still remains elusive for settings with two or more items. In this work, we initiate the exploration of the use of tools from deep learning for the automated design of optimal auctions. We model an auction as a multi-layer neural network, frame optimal auction design as a constrained learning problem, and show how it can be solved using standard machine learning pipelines. In addition to providing generalization bounds, we present extensive experimental results, recovering essentially all known solutions that come from the theoretical analysis of optimal auction design problems and obtaining novel mechanisms for settings in which the optimal mechanism is unknown. [ABSTRACT FROM AUTHOR]

Cyberattacks have been increasing in volume and intensity, necessitating proactive measures. Cybersecurity risk management frameworks are deployed to provide actionable intelligence to mitigate potential threats by analyzing the available cybersecurity data. Existing frameworks, such as MITRE ATT&CK, provide timely mitigation strategies against attacker capabilities yet do not account for hacker data when developing cyber threat intelligence. Therefore, we developed a novel information technology artifact, ATT&CK-Link, which incorporates a novel transformer and multi-teacher knowledge distillation design, to link hacker threats to this broadly used framework. Here, we illustrated how hospital systems can use this framework to proactively protect their cyberinfrastructure against hacker threats. Our ATT&CK-Link framework has practical implications for cybersecurity professionals, who can implement our framework to generate strategic, operational, and tactical cyber threat intelligence. ATT&CK-Link also contributes to the information systems knowledge base by providing design principles to pursue targeted cybersecurity analytics, risk management, and broader text analytics research through simultaneous multi-modal (e.g., text and code) distillation and classification. [ABSTRACT FROM AUTHOR]

This paper considers a multi-period multi-product capacitated lot-sizing problem. It develops an integrated predictive maintenance and production planning framework using deep learning and mathematical programming. The objective is to minimise the sum of maintenance, setup, holding, backorder, and production costs, while satisfying the demand for all products over the horizon under consideration. Based on a rolling horizon approach, the model dynamically integrates data-driven predictive maintenance and production planning. The used maintenance policy includes replacements and minimal repairs that are considered as preventive and corrective maintenance, respectively. To select preventive maintenance actions, a long short-term memory model is employed to accurately predict the health condition of the machine. Each rolling horizon consists of ordinary and forecast stages, and by collecting new sensor data, the maintenance and production decisions are simultaneously updated. The resulting integrated framework is validated using a benchmarking data set. The results are compared for different approaches to highlight the advantages of the proposed framework. [ABSTRACT FROM AUTHOR]

Fault diagnosis is an indispensable basis for the collaborative maintenance in prognostic and health management. Most of existing data-driven fault diagnosis approaches are designed in the framework of supervised learning, which requires a large number of labelled samples. In this paper, a novel self-training semi-supervised deep learning (SSDL) approach is proposed to train a fault diagnosis model together with few labelled and abundant unlabelled samples. The addressed SSDL approach is realised by initialising a stacked sparse auto-encoder classifier using the labelled samples, and subsequently updating the classifier via sampling a few candidates with most reliable pseudo labels from the unlabelled samples step by step. Unlike the commonly used static sampling strategy in existing self-training semi-supervised frameworks, a gradually exploiting mechanism is proposed in SSDL to increase the number of selected pseudo-labelled candidates gradually. In addition, instead of using the prediction accuracy as the confidence estimation for pseudo-labels, a distance-based sampling criterion is designed to assign the label for each unlabelled sample by its nearest labelled sample based on their Euclidean distances in the deep feature space. The experimental results show that the proposed SSDL approach can achieve good prediction accuracy compared to other self-training semi-supervised learning algorithms. [ABSTRACT FROM AUTHOR]

The erosion of high-end fashion brands by fast-fashion copycats (e.g., Zara, H&M) has stirred controversies and unceasing legal attempts to copyright fashion designs. Despite the purported negative impact of copycats, the effect of fashion copycats on high-end brands remains empirically unclear. Research on this topic has been impeded by the absence of a modeling framework to quantify fashion and by the lack of consumer-level data on fashion choices. The authors collect data on the posting behaviors of consumers on a fashion-specific social media platform and develop a dynamic structural model with deep learning image analytics to characterize consumers' choices of brands and styles. Results suggest that fast-fashion copycats can both harm high-end brands (a cannibalization effect) and help them (a market expansion effect). The authors also identify both static and dynamic mechanisms that contribute to the market expansion effect: The affordability of mixing copycats with high-end brands boosts the number of high-end items featured in posts by financially constrained consumers (a static mechanism). In addition, good styles from copycats enable users to build their popularity on social media over time, which may increase the users' valuation of high-end brands and reduce the users' future costs via sponsorship opportunities (dynamic mechanisms). The results could inform policy makers about the potential consequences of prohibiting fashion copycats. [ABSTRACT FROM AUTHOR]

Many machine learning applications in bioinformatics currently rely on matching gene identities when analyzing input gene signatures and fail to take advantage of preexisting knowledge about gene functions. To further enable comparative analysis of OMICS datasets, including target deconvolution and mechanism of action studies, we develop an approach that represents gene signatures projected onto their biological functions, instead of their identities, similar to how the word2vec technique works in natural language processing. We develop the Functional Representation of Gene Signatures (FRoGS) approach by training a deep learning model and demonstrate that its application to the Broad Institutes L1000 datasets results in more effective compound-target predictions than models based on gene identities alone. By integrating additional pharmacological activity data sources, FRoGS significantly increases the number of high-quality compound-target predictions relative to existing approaches, many of which are supported by in silico and/or experimental evidence. These results underscore the general utility of FRoGS in machine learning-based bioinformatics applications. Prediction networks pre-equipped with the knowledge of gene functions may help uncover new relationships among gene signatures acquired by large-scale OMICs studies on compounds, cell types, disease models, and patient cohorts.

Differences in gait patterns of children with Duchenne muscular dystrophy (DMD) and typically developing (TD) peers are visible to the eye, but quantifications of those differences outside of the gait laboratory have been elusive. In this work, we measured vertical, mediolateral, and anteroposterior acceleration using a waist-worn iPhone accelerometer during ambulation across a typical range of velocities. Fifteen TD and fifteen DMD children from 3 to 16 years of age underwent eight walking/running activities, including five 25 m walk/run speed-calibration tests at a slow walk to running speeds (SC-L1 to SC-L5), a 6-min walk test (6MWT), a 100 m fast walk/jog/run (100MRW), and a free walk (FW). For clinical anchoring purposes, participants completed a Northstar Ambulatory Assessment (NSAA). We extracted temporospatial gait clinical features (CFs) and applied multiple machine learning (ML) approaches to differentiate between DMD and TD children using extracted temporospatial gait CFs and raw data. Extracted temporospatial gait CFs showed reduced step length and a greater mediolateral component of total power (TP) consistent with shorter strides and Trendelenberg-like gait commonly observed in DMD. ML approaches using temporospatial gait CFs and raw data varied in effectiveness at differentiating between DMD and TD controls at different speeds, with an accuracy of up to 100%. We demonstrate that by using ML with accelerometer data from a consumer-grade smartphone, we can capture DMD-associated gait characteristics in toddlers to teens.

The development of high-resolution microscopes has made it possible to investigate cellular processes in 3D and over time. However, observing fast cellular dynamics remains challenging because of photobleaching and phototoxicity. Here we report the implementation of two content-aware frame interpolation (CAFI) deep learning networks, Zooming SlowMo and Depth-Aware Video Frame Interpolation, that are highly suited for accurately predicting images in between image pairs, therefore improving the temporal resolution of image series post-acquisition. We show that CAFI is capable of understanding the motion context of biological structures and can perform better than standard interpolation methods. We benchmark CAFIs performance on 12 different datasets, obtained from four different microscopy modalities, and demonstrate its capabilities for single-particle tracking and nuclear segmentation. CAFI potentially allows for reduced light exposure and phototoxicity on the sample for improved long-term live-cell imaging. The models and the training and testing data are available via the ZeroCostDL4Mic platform.

Many peptide hormones form an α-helix on binding their receptors1-4, and sensitive methods for their detection could contribute to better clinical management of disease5. De novo protein design can now generate binders with high affinity and specificity to structured proteins6,7. However, the design of interactions between proteins and short peptides with helical propensity is an unmet challenge. Here we describe parametric generation and deep learning-based methods for designing proteins to address this challenge. We show that by extending RFdiffusion8 to enable binder design to flexible targets, and to refining input structure models by successive noising and denoising (partial diffusion), picomolar-affinity binders can be generated to helical peptide targets by either refining designs generated with other methods, or completely de novo starting from random noise distributions without any subsequent experimental optimization. The RFdiffusion designs enable the enrichment and subsequent detection of parathyroid hormone and glucagon by mass spectrometry, and the construction of bioluminescence-based protein biosensors. The ability to design binders to conformationally variable targets, and to optimize by partial diffusion both natural and designed proteins, should be broadly useful.

Soft biological tissues often have complex mechanical properties due to variation in structural components. In this paper, we develop a novel UNet-based neural network model for inversion in elasticity (El-UNet) to infer the spatial distributions of mechanical parameters from strain maps as input images, normal stress boundary conditions, and domain physics information. We show superior performance - both in terms of accuracy and computational cost - by El-UNet compared to fully-connected physics-informed neural networks in estimating unknown parameters and stress distributions for isotropic linear elasticity. We characterize different variations of El-UNet and propose a self-adaptive spatial loss weighting approach. To validate our inversion models, we performed various finite-element simulations of isotropic domains with heterogenous distributions of material parameters to generate synthetic data. El-UNet is faster and more accurate than the fully-connected physics-informed implementation in resolving the distribution of unknown fields. Among the tested models, the self-adaptive spatially weighted models had the most accurate reconstructions in equal computation times. The learned spatial weighting distribution visibly corresponded to regions that the unweighted models were resolving inaccurately. Our work demonstrates a computationally efficient inversion algorithm for elasticity imaging using convolutional neural networks and presents a potential fast framework for three-dimensional inverse elasticity problems that have proven unachievable through previously proposed methods.

PurposeTo develop and evaluate a deep learning (DL) model to assess fundus photograph quality, and quantitatively measure its impact on automated POAG detection in independent study populations.MethodsImage quality ground truth was determined by manual review of 2815 fundus photographs of healthy and POAG eyes from the Diagnostic Innovations in Glaucoma Study and African Descent and Glaucoma Evaluation Study (DIGS/ADAGES), as well as 11,350 from the Ocular Hypertension Treatment Study (OHTS). Human experts assessed a photograph as high quality if of sufficient quality to determine POAG status and poor quality if not. A DL quality model was trained on photographs from DIGS/ADAGES and tested on OHTS. The effect of DL quality assessment on DL POAG detection was measured using area under the receiver operating characteristic (AUROC).ResultsThe DL quality model yielded an AUROC of 0.97 for differentiating between high- and low-quality photographs; qualitative human review affirmed high model performance. Diagnostic accuracy of the DL POAG model was significantly greater (P < 0.001) in good (AUROC, 0.87; 95% CI, 0.80-0.92) compared with poor quality photographs (AUROC, 0.77; 95% CI, 0.67-0.88).ConclusionsThe DL quality model was able to accurately assess fundus photograph quality. Using automated quality assessment to filter out low-quality photographs increased the accuracy of a DL POAG detection model.Translational relevanceIncorporating DL quality assessment into automated review of fundus photographs can help to decrease the burden of manual review and improve accuracy for automated DL POAG detection.

Deep learning shows promise for automating detection and classification of wildlife from digital aerial imagery to support cost-efficient remote sensing solutions for wildlife population monitoring. To support in-flight orthorectification and machine learning processing to detect and classify wildlife from imagery in near real-time, we evaluated deep learning methods that address hardware limitations and the need for processing efficiencies to support the envisioned in-flight workflow. We developed an annotated dataset for a suite of marine birds from high-resolution digital aerial imagery collected over open water environments to train the models. The proposed 3-stage workflow for automated, in-flight data processing includes: 1) image filtering based on the probability of any bird occurrence, 2) bird instance detection, and 3) bird instance classification. For image filtering, we compared the performance of a binary classifier with Mask Region-based Convolutional Neural Network (Mask R-CNN) as a means of sub-setting large volumes of imagery based on the probability of at least one bird occurrence in an image. On both the validation and test datasets, the binary classifier achieved higher performance than Mask R-CNN for predicting bird occurrence at the image-level. We recommend the binary classifier over Mask R-CNN for workflow first-stage filtering. For bird instance detection, we leveraged Mask R-CNN as our detection framework and proposed an iterative refinement method to bootstrap our predicted detections from loose ground-truth annotations. We also discuss future work to address the taxonomic classification phase of the envisioned workflow.

PURPOSE: To investigate the use of super-resolution imaging techniques to enable telepathology using low-cost commercial cameras. DESIGN: Experimental study. PARTICIPANTS: A total of 139 ophthalmic pathology slides obtained from the Ophthalmic Pathology service at the University of California, Irvine. METHODS: Denoising Diffusion Probabilistic Model (DDPM) was developed to predict super-resolution pathology slide images from low-resolution inputs. The model was pretrained using 150 000 images randomly sampled from the ImageNet dataset. Patch aggregation was used to generate large images with DDPM. The performance of DDPM was evaluated against that of generative adversarial networks (GANs) and Robust UNet, which were also trained on the same dataset. MAIN OUTCOME MEASURES: The performance of models trained to generate super-resolution output images from low-resolution input images can be evaluated by using the mean squared error (MSE) and Structural Similarity Index Measure (SSIM), as well as subjective grades provided by expert pathologist graders. RESULTS: In total, our study included 110 training images, 9 validation images, and 20 testing images. The objective performance scores were averaged over patches generated from 20 test images. The DDPM-based approach with pretraining produced the best results, with an MSE score of 1.35e-5 and an SSIM score of 0.8987. A qualitative analysis of super-resolution images was conducted by expert 3 pathologists and 1 expert ophthalmic microscopist, and the average accuracy of identifying the correct ground truth images ranged from 25% to 70% (with an average accuracy of 46.5%) for widefield images and 25% to 60% (with an average accuracy of 38.25%) for individual patches. CONCLUSIONS: The DDPM-based approach with pretraining is assessed to be effective at super-resolution prediction for ophthalmic pathology slides both in terms of objective and subjective measures. The proposed methodology is expected to decrease the reliance on costly slide scanners for acquiring high-quality pathology slide images, while also streamlining clinical workflow and expanding the scope of ophthalmic telepathology. FINANCIAL DISCLOSURES: Proprietary or commercial disclosure may be found in the Footnotes and Disclosures at the end of this article.

A longitudinal ophthalmic dataset was used to investigate multi-modal machine learning (ML) models incorporating patient demographics and history, clinical measurements, optical coherence tomography (OCT), and visual field (VF) testing in predicting glaucoma surgical interventions. The cohort included 369 patients who underwent glaucoma surgery and 592 patients who did not undergo surgery. The data types used for prediction included patient demographics, history of systemic conditions, medication history, ophthalmic measurements, 24-2 VF results, and thickness measurements from OCT imaging. The ML models were trained to predict surgical interventions and evaluated on independent data collected at a separate study site. The models were evaluated based on their ability to predict surgeries at varying lengths of time prior to surgical intervention. The highest performing predictions achieved an AUC of 0.93, 0.92, and 0.93 in predicting surgical intervention at 1 year, 2 years, and 3 years, respectively. The models were also able to achieve high sensitivity (0.89, 0.77, 0.86 at 1, 2, and 3 years, respectively) and specificity (0.85, 0.90, and 0.91 at 1, 2, and 3 years, respectively) at an 0.80 level of precision. The multi-modal models trained on a combination of data types predicted surgical interventions with high accuracy up to three years prior to surgery and could provide an important tool to predict the need for glaucoma intervention.

BACKGROUND: Magnetic resonance image only (MRI-only) simulation for head and neck (H&N) radiotherapy (RT) could allow for single-image modality planning with excellent soft tissue contrast. In the MRI-only simulation workflow, synthetic computed tomography (sCT) is generated from MRI to provide electron density information for dose calculation. Bone/air regions produce little MRI signal which could lead to electron density misclassification in sCT. Establishing the dosimetric impact of this error could inform quality assurance (QA) procedures using MRI-only RT planning or compensatory methods for accurate dosimetric calculation. PURPOSE: The aim of this study was to investigate if Hounsfield unit (HU) voxel misassignments from sCT images result in dosimetric errors in clinical treatment plans. METHODS: Fourteen H&N cancer patients undergoing same-day CT and 3T MRI simulation were retrospectively identified. MRI was deformed to the CT using multimodal deformable image registration. sCTs were generated from T1w DIXON MRIs using a commercially available deep learning-based generator (MRIplanner, Spectronic Medical AB, Helsingborg, Sweden). Tissue voxel assignment was quantified by creating a CT-derived HU threshold contour. CT/sCT HU differences for anatomical/target contours and tissue classification regions including air (500 HU) were quantified. t-test was used to determine if sCT/CT HU differences were significant. The frequency of structures that had a HU difference > 80 HU (the CT window-width setting for intra-cranial structures) was computed to establish structure classification accuracy. Clinical intensity modulated radiation therapy (IMRT) treatment plans created on CT were retrospectively recalculated on sCT images and compared using the gamma metric. RESULTS: The mean ratio of sCT HUs relative to CT for air, adipose tissue, soft tissue, spongy and cortical bone were 1.7 ± 0.3, 1.1 ± 0.1, 1.0 ± 0.1, 0.9 ± 0.1 and 0.8 ± 0.1 (value of 1 indicates perfect agreement). T-tests (significance set at t = 0.05) identified differences in HU values for air, spongy and cortical bone in sCT images compared to CT. The structures with sCT/CT HU differences > 80 HU of note were the left and right (L/R) cochlea and mandible (>79% of the tested cohort), the oral cavity (for 57% of the tested cohort), the epiglottis (for 43% of the tested cohort) and the L/R TM joints (occurring > 29% of the cohort). In the case of the cochlea and TM joints, these structures contain dense bone/air interfaces. In the case of the oral cavity and mandible, these structures suffer the additional challenge of being positionally altered in CT versus MRI simulation (due to a non-MR safe immobilizing bite block requiring absence of bite block in MR). Finally, the epiglottis HU assignment suffers from its small size and unstable positionality. Plans recalculated on sCT yielded global/local gamma pass rates of 95.5% ± 2% (3 mm, 3%) and 92.7% ± 2.1% (2 mm, 2%). The largest mean differences in D95, Dmean , D50 dose volume histogram (DVH) metrics for organ-at-risk (OAR) and planning tumor volumes (PTVs) were 2.3% ± 3.0% and 0.7% ± 1.9% respectively. CONCLUSIONS: In this cohort, HU differences of CT and sCT were observed but did not translate into a reduction in gamma pass rates or differences in average PTV/OAR dose metrics greater than 3%. For sites such as the H&N where there are many tissue interfaces we did not observe large scale dose deviations but further studies using larger retrospective cohorts are merited to establish the variation in sCT dosimetric accuracy which could help to inform QA limits on clinical sCT usage.

A 2D U-Net was trained to generate synthetic T1p maps from T2 maps for knee MRI to explore the feasibility of domain adaptation for enriching existing datasets and enabling rapid, reliable image reconstruction. The network was developed using 509 healthy contralateral and injured ipsilateral knee images from patients with ACL injuries and reconstruction surgeries acquired across three institutions. Network generalizability was evaluated on 343 knees acquired in a clinical setting and 46 knees from simultaneous bilateral acquisition in a research setting. The deep neural network synthesized high-fidelity reconstructions of T1p maps, preserving textures and local T1p elevation patterns in cartilage with a normalized mean square error of 2.4% and Pearsons correlation coefficient of 0.93. Analysis of reconstructed T1p maps within cartilage compartments revealed minimal bias (-0.10 ms), tight limits of agreement, and quantification error (5.7%) below the threshold for clinically significant change (6.42%) associated with osteoarthritis. In an out-of-distribution external test set, synthetic maps preserved T1p textures, but exhibited increased bias and wider limits of agreement. This study demonstrates the capability of image synthesis to reduce acquisition time, derive meaningful information from existing datasets, and suggest a pathway for standardizing T1p as a quantitative biomarker for osteoarthritis.

Recent advances in single-cell technologies have led to the discovery of thousands of brain cell types; however, our understanding of the gene regulatory programs in these cell types is far from complete1-4. Here we report a comprehensive atlas of candidate cis-regulatory DNA elements (cCREs) in the adult mouse brain, generated by analysing chromatin accessibility in 2.3 million individual brain cells from 117 anatomical dissections. The atlas includes approximately 1 million cCREs and their chromatin accessibility across 1,482 distinct brain cell populations, adding over 446,000 cCREs to the most recent such annotation in the mouse genome. The mouse brain cCREs are moderately conserved in the human brain. The mouse-specific cCREs-specifically, those identified from a subset of cortical excitatory neurons-are strongly enriched for transposable elements, suggesting a potential role for transposable elements in the emergence of new regulatory programs and neuronal diversity. Finally, we infer the gene regulatory networks in over 260 subclasses of mouse brain cells and develop deep-learning models to predict the activities of gene regulatory elements in different brain cell types from the DNA sequence alone. Our results provide a resource for the analysis of cell-type-specific gene regulation programs in both mouse and human brains.

PURPOSE: Two-dimensional radiotherapy is often used to treat cervical cancer in low- and middle-income countries, but treatment planning can be challenging and time-consuming. Neural networks offer the potential to greatly decrease planning time through automation, but the impact of the wide range of hyperparameters to be set during training on model accuracy has not been exhaustively investigated. In the current study, we evaluated the effect of several convolutional neural network architectures and hyperparameters on 2D radiotherapy treatment field delineation. METHODS: Six commonly used deep learning architectures were trained to delineate four-field box apertures on digitally reconstructed radiographs for cervical cancer radiotherapy. A comprehensive search of optimal hyperparameters for all models was conducted by varying the initial learning rate, image normalization methods, and (when appropriate) convolutional kernel size, the number of learnable parameters via network depth and the number of feature maps per convolution, and nonlinear activation functions. This yielded over 1700 unique models, which were all trained until performance converged and then tested on a separate dataset. RESULTS: Of all hyperparameters, the choice of initial learning rate was most consistently significant for improved performance on the test set, with all top-performing models using learning rates of 0.0001. The optimal image normalization was not consistent across architectures. High overlap (mean Dice similarity coefficient = 0.98) and surface distance agreement (mean surface distance

BACKGROUND: Recent advances in data-driven computational approaches have been helpful in devising tools to objectively diagnose psychiatric disorders. However, current machine learning studies limited to small homogeneous samples, different methodologies, and different imaging collection protocols, limit the ability to directly compare and generalize their results. Here we aimed to classify individuals with PTSD versus controls and assess the generalizability using a large heterogeneous brain datasets from the ENIGMA-PGC PTSD Working group. METHODS: We analyzed brain MRI data from 3,477 structural-MRI; 2,495 resting state-fMRI; and 1,952 diffusion-MRI. First, we identified the brain features that best distinguish individuals with PTSD from controls using traditional machine learning methods. Second, we assessed the utility of the denoising variational autoencoder (DVAE) and evaluated its classification performance. Third, we assessed the generalizability and reproducibility of both models using leave-one-site-out cross-validation procedure for each modality. RESULTS: We found lower performance in classifying PTSD vs. controls with data from over 20 sites (60 % test AUC for s-MRI, 59 % for rs-fMRI and 56 % for d-MRI), as compared to other studies run on single-site data. The performance increased when classifying PTSD from HC without trauma history in each modality (75 % AUC). The classification performance remained intact when applying the DVAE framework, which reduced the number of features. Finally, we found that the DVAE framework achieved better generalization to unseen datasets compared with the traditional machine learning frameworks, albeit performance was slightly above chance. CONCLUSION: These results have the potential to provide a baseline classification performance for PTSD when using large scale neuroimaging datasets. Our findings show that the control group used can heavily affect classification performance. The DVAE framework provided better generalizability for the multi-site data. This may be more significant in clinical practice since the neuroimaging-based diagnostic DVAE classification models are much less site-specific, rendering them more generalizable.

KEY POINTS: The authors leverage the unique benefits of panoptic segmentation to perform the largest ever quantitation of reference kidney morphometry. Kidney features vary with age and sex; and glomeruli size may intricately link to creatinine, defying prior notions. BACKGROUND: Reference histomorphometric data of healthy human kidneys are largely lacking because of laborious quantitation requirements. Correlating histomorphometric features with clinical parameters through machine learning approaches can provide valuable information about natural population variance. To this end, we leveraged deep learning (DL), computational image analysis, and feature analysis to associate the relationship of histomorphometry with patient age, sex, serum creatinine (SCr), and eGFR in a multinational set of reference kidney tissue sections. METHODS: A panoptic segmentation neural network was developed and used to segment viable and sclerotic glomeruli, cortical and medullary interstitia, tubules, and arteries/arterioles in the digitized images of 79 periodic acid–Schiff-stained human nephrectomy sections showing minimal pathologic changes. Simple morphometrics (e.g., area, radius, density) were quantified from the segmented classes. Regression analysis aided in determining the association of histomorphometric parameters with age, sex, SCr, and eGFR. RESULTS: Our DL model achieved high segmentation performance for all test compartments. The size and density of glomeruli, tubules, and arteries/arterioles varied significantly among healthy humans, with potentially large differences between geographically diverse patients. Glomerular size was significantly correlated with SCr and eGFR. Slight, albeit significant, differences in renal vasculature were observed between sexes. Glomerulosclerosis percentage increased, and cortical density of arteries/arterioles decreased, as a function of increasing age. CONCLUSIONS: Using DL, we automated precise measurements of kidney histomorphometric features. In the reference kidney tissue, several histomorphometric features demonstrated significant correlation to patient demographics, SCr, and eGFR. DL tools can increase the efficiency and rigor of histomorphometric analysis.

Biobanks that collect deep phenotypic and genomic data across many individuals have emerged as a key resource in human genetics. However, phenotypes in biobanks are often missing across many individuals, limiting their utility. We propose AutoComplete, a deep learning-based imputation method to impute or fill-in missing phenotypes in population-scale biobank datasets. When applied to collections of phenotypes measured across ~300,000 individuals from the UK Biobank, AutoComplete substantially improved imputation accuracy over existing methods. On three traits with notable amounts of missingness, we show that AutoComplete yields imputed phenotypes that are genetically similar to the originally observed phenotypes while increasing the effective sample size by about twofold on average. Further, genome-wide association analyses on the resulting imputed phenotypes led to a substantial increase in the number of associated loci. Our results demonstrate the utility of deep learning-based phenotype imputation to increase power for genetic discoveries in existing biobank datasets.

Genomic deep learning models can predict genome-wide epigenetic features and gene expression levels directly from DNA sequence. While current models perform well at predicting gene expression levels across genes in different cell types from the reference genome, their ability to explain expression variation between individuals due to cis-regulatory genetic variants remains largely unexplored. Here, we evaluate four state-of-the-art models on paired personal genome and transcriptome data and find limited performance when explaining variation in expression across individuals. In addition, models often fail to predict the correct direction of effect of cis-regulatory genetic variation on expression.

BACKGROUND: Artificial intelligence (AI) has demonstrated significant potential in supporting emergency medical services personnel during out-of-hospital cardiac arrest (OHCA) care; however, the extent of research evaluating this topic is unknown. This scoping review examines the breadth of literature on the application of AI in early OHCA care. METHODS: We conducted a search of PubMed®, Embase, and Web of Science in accordance with the Preferred Reporting Items for Systematic Reviews and Meta-Analyses Extension for Scoping Reviews guidelines. Articles focused on non-traumatic OHCA and published prior to January 18th, 2023 were included. Studies were excluded if they did not use an AI intervention (including machine learning, deep learning, or natural language processing), or did not utilize data from the prehospital phase of care. RESULTS: Of 173 unique articles identified, 54 (31%) were included after screening. Of these studies, 15 (28%) were from the year 2022 and with an increasing trend annually starting in 2019. The majority were carried out by multinational collaborations (20/54, 38%) with additional studies from the United States (10/54, 19%), Korea (5/54, 10%), and Spain (3/54, 6%). Studies were classified into three major categories including ECG waveform classification and outcome prediction (24/54, 44%), early dispatch-level detection and outcome prediction (7/54, 13%), return of spontaneous circulation and survival outcome prediction (15/54, 20%), and other (9/54, 16%). All but one study had a retrospective design. CONCLUSIONS: A small but growing body of literature exists describing the use of AI to augment early OHCA care.