Increasing resolution in stress neurobiology: from single cells to complex group behaviors.

Stress can have severe psychological and physiological consequences. Thus, inappropriate regulation of the stress response is linked to the etiology of mood and anxiety disorders. The generation and implementation of preclinical animal models represent valuable tools to explore and characterize the mechanisms underlying the pathophysiology of stress-related psychiatric disorders and the development of novel pharmacological strategies. In this commentary, we discuss the strengths and limitations of state-of-the-art molecular and computational advances employed in stress neurobiology research, with a focus on the ever-increasing spatiotemporal resolution in cell biology and behavioral science. Finally, we share our perspective on future directions in the fields of preclinical and human stress research.

Quantifying changes in societal optimism from online sentiment.

Individuals can hold contrasting views about distinct times: for example, dread over tomorrow's appointment and excitement about next summer's vacation. Yet, psychological measures of optimism often assess only one time point or ask participants to generalize about their future. Here, we address these limitations by developing the optimism curve, a measure of societal optimism that compares positivity toward different future times that was inspired by the Treasury bond yield curve. By performing sentiment analysis on over 3.5 million tweets that reference 23 future time points (2 days to 30 years), we measured how positivity differs across short-, medium-, and longer-term future references. We found a consistent negative association between positivity and the distance into the future referenced: From August 2017 to February 2020, the long-term future was discussed less positively than the short-term future. During the COVID-19 pandemic, this relationship inverted, indicating declining near-future- but stable distant-future-optimism. Our results demonstrate that individuals hold differentiated attitudes toward the near and distant future that shift in aggregate over time in response to external events. The optimism curve uniquely captures these shifting attitudes and may serve as a useful tool that can expand existing psychometric measures of optimism.

Predicting epidemics using search engine data: a comparative study on measles in the largest countries of Europe.

BACKGROUND: In recent years new forms of syndromic surveillance that use data from the Internet have been proposed. These have been developed to assist the early prediction of epidemics in various cases and diseases. It has been found that these systems are accurate in monitoring and predicting outbreaks before these are observed in population and, therefore, they can be used as a complement to other methods. In this research, our aim is to examine a highly infectious disease, measles, as there is no extensive literature on forecasting measles using Internet data, METHODS: This research has been conducted with official data on measles for 5 years (2013-2018) from the competent authority of the European Union (European Center of Disease and Prevention - ECDC) and data obtained from Google Trends by using scripts coded in Python. We compared regression models forecasting the development of measles in the five countries. RESULTS: Results show that measles can be estimated and predicted through Google Trends in terms of time, volume and the overall spread. The combined results reveal a strong relationship of measles cases with the predicted cases (correlation coefficient R= 0.779 in two-tailed significance p< 0.01). The mean standard error was relatively low 45.2 (12.19%) for the combined results. However, major differences and deviations were observed for countries with a relatively low impact of measles, such as the United Kingdom and Spain. For these countries, alternative models were tested in an attempt to improve the results. CONCLUSIONS: The estimation of measles cases from Google Trends produces acceptable results and can help predict outbreaks in a robust and sound manner, at least 2 months in advance. Python scripts can be used individually or within the framework of an integrated Internet surveillance system for tracking epidemics as the one addressed here.

Falkner-Skan Flow with Stream-Wise Pressure Gradient and Transfer of Mass over a Dynamic Wall.

In this work, an important model in fluid dynamics is analyzed by a new hybrid neurocomputing algorithm. We have considered the Falkner-Skan (FS) with the stream-wise pressure gradient transfer of mass over a dynamic wall. To analyze the boundary flow of the FS model, we have utilized the global search characteristic of a recently developed heuristic, the Sine Cosine Algorithm (SCA), and the local search characteristic of Sequential Quadratic Programming (SQP). Artificial neural network (ANN) architecture is utilized to construct a series solution of the mathematical model. We have called our technique the ANN-SCA-SQP algorithm. The dynamic of the FS system is observed by varying stream-wise pressure gradient mass transfer and dynamic wall. To validate the effectiveness of ANN-SCA-SQP algorithm, our solutions are compared with state-of-the-art reference solutions. We have repeated a hundred experiments to establish the robustness of our approach. Our experimental outcome validates the superiority of the ANN-SCA-SQP algorithm.

Exascale applications: skin in the game.

As noted in Wikipedia, skin in the game refers to having 'incurred risk by being involved in achieving a goal', where 'skin is a synecdoche for the person involved, and game is the metaphor for actions on the field of play under discussion'. For exascale applications under development in the US Department of Energy Exascale Computing Project, nothing could be more apt, with the skin being exascale applications and the game being delivering comprehensive science-based computational applications that effectively exploit exascale high-performance computing technologies to provide breakthrough modelling and simulation and data science solutions. These solutions will yield high-confidence insights and answers to the most critical problems and challenges for the USA in scientific discovery, national security, energy assurance, economic competitiveness and advanced healthcare. This article is part of a discussion meeting issue 'Numerical algorithms for high-performance computational science'.

Artificial Intelligence for Modeling Real Estate Price Using Call Detail Records and Hybrid Machine Learning Approach.

Advancement of accurate models for predicting real estate price is of utmost importance for urban development and several critical economic functions. Due to the significant uncertainties and dynamic variables, modeling real estate has been studied as complex systems. In this study, a novel machine learning method is proposed to tackle real estate modeling complexity. Call detail records (CDR) provides excellent opportunities for in-depth investigation of the mobility characterization. This study explores the CDR potential for predicting the real estate price with the aid of artificial intelligence (AI). Several essential mobility entropy factors, including dweller entropy, dweller gyration, workers' entropy, worker gyration, dwellers' work distance, and workers' home distance, are used as input variables. The prediction model is developed using the machine learning method of multi-layered perceptron (MLP) trained with the evolutionary algorithm of particle swarm optimization (PSO). Model performance is evaluated using mean square error (MSE), sustainability index (SI), and Willmott's index (WI). The proposed model showed promising results revealing that the workers' entropy and the dwellers' work distances directly influence the real estate price. However, the dweller gyration, dweller entropy, workers' gyration, and the workers' home had a minimum effect on the price. Furthermore, it is shown that the flow of activities and entropy of mobility are often associated with the regions with lower real estate prices.

Artificial intelligence: A joint narrative on potential use in pediatric stem and immune cell therapies and regenerative medicine.

Artificial Intelligence (AI) reflects the intelligence exhibited by machines and software. It is a highly desirable academic field of many current fields of studies. Leading AI researchers describe the field as "the study and design of intelligent agents". McCarthy invented this term in 1955 and defined it as "the science and engineering of making intelligent machines". The central goals of AI research are reasoning, knowledge, planning, learning, natural language processing (communication), perception and the ability to move and manipulate objects. In fact the multidisplinary AI field is considered to be rather interdisciplinary covering numerous number of sciences and professions, including computer science, psychology, linguistics, philosophy and neurosciences. The field was founded on the claim that a central intellectual property of humans, intelligence-the sapience of Homo Sapiens "can be so precisely described that a machine can be made to simulate it". This raises philosophical issues about the nature of the mind and the ethics of creating artificial beings endowed with human-like intelligence. Artificial Intelligence has been the subject of tremendous optimism but has also suffered stunning setbacks. The goal of this narrative is to review the potential use of AI approaches and their integration into pediatric cellular therapies and regenerative medicine. Emphasis is placed on recognition and application of AI techniques in the development of predictive models for personalized treatments with engineered stem cells, immune cells and regenerated tissues in adults and children. These intelligent machines could dissect the whole genome and isolate the immune particularities of individual patient's disease in a matter of minutes and create the treatment that is customized to patient's genetic specificity and immune system capability. AI techniques could be used for optimization of clinical trials of innovative stem cell and gene therapies in pediatric patients by precise planning of treatments, predicting clinical outcomes, simplifying recruitment and retention of patients, learning from input data and applying to new data, thus lowering their complexity and costs. Complementing human intelligence with machine intelligence could have an exponentially high impact on continual progress in many fields of pediatrics. However how long before we could see the real impact still remains the big question. The most pertinent question that remains to be answered therefore, is can AI effectively and accurately predict properties of newer DDR strategies? The goal of this article is to review the use of AI method for cellular therapy and regenerative medicine and emphasize its potential to further the progress in these fields of medicine.

We get the algorithms of our ground truths: Designing referential databases in digital image processing.

This article documents the practical efforts of a group of scientists designing an image-processing algorithm for saliency detection. By following the actors of this computer science project, the article shows that the problems often considered to be the starting points of computational models are in fact provisional results of time-consuming, collective and highly material processes that engage habits, desires, skills and values. In the project being studied, problematization processes lead to the constitution of referential databases called 'ground truths' that enable both the effective shaping of algorithms and the evaluation of their performances. Working as important common touchstones for research communities in image processing, the ground truths are inherited from prior problematization processes and may be imparted to subsequent ones. The ethnographic results of this study suggest two complementary analytical perspectives on algorithms: (1) an 'axiomatic' perspective that understands algorithms as sets of instructions designed to solve given problems computationally in the best possible way, and (2) a 'problem-oriented' perspective that understands algorithms as sets of instructions designed to computationally retrieve outputs designed and designated during specific problematization processes. If the axiomatic perspective on algorithms puts the emphasis on the numerical transformations of inputs into outputs, the problem-oriented perspective puts the emphasis on the definition of both inputs and outputs.

Empowering deep neural quantum states through efficient optimization.

Computing the ground state of interacting quantum matter is a long-standing challenge, especially for complex two-dimensional systems. Recent developments have highlighted the potential of neural quantum states to solve the quantum many-body problem by encoding the many-body wavefunction into artificial neural networks. However, this method has faced the critical limitation that existing optimization algorithms are not suitable for training modern large-scale deep network architectures. Here, we introduce a minimum-step stochastic-reconfiguration optimization algorithm, which allows us to train deep neural quantum states with up to 106 parameters. We demonstrate our method for paradigmatic frustrated spin-1/2 models on square and triangular lattices, for which our trained deep networks approach machine precision and yield improved variational energies compared to existing results. Equipped with our optimization algorithm, we find numerical evidence for gapless quantum-spin-liquid phases in the considered models, an open question to date. We present a method that captures the emergent complexity in quantum many-body problems through the expressive power of large-scale artificial neural networks.

Weak signal extraction enabled by deep neural network denoising of diffraction data.

The removal or cancellation of noise has wide-spread applications in imaging and acoustics. In applications in everyday life, such as image restoration, denoising may even include generative aspects, which are unfaithful to the ground truth. For scientific use, however, denoising must reproduce the ground truth accurately. Denoising scientific data is further challenged by unknown noise profiles. In fact, such data will often include noise from multiple distinct sources, which substantially reduces the applicability of simulation-based approaches. Here we show how scientific data can be denoised by using a deep convolutional neural network such that weak signals appear with quantitative accuracy. In particular, we study X-ray diffraction and resonant X-ray scattering data recorded on crystalline materials. We demonstrate that weak signals stemming from charge ordering, insignificant in the noisy data, become visible and accurate in the denoised data. This success is enabled by supervised training of a deep neural network with pairs of measured low- and high-noise data. We additionally show that using artificial noise does not yield such quantitatively accurate results. Our approach thus illustrates a practical strategy for noise filtering that can be applied to challenging acquisition problems.

Experimental demonstration of magnetic tunnel junction-based computational random-access memory.

The conventional computing paradigm struggles to fulfill the rapidly growing demands from emerging applications, especially those for machine intelligence because much of the power and energy is consumed by constant data transfers between logic and memory modules. A new paradigm, called "computational random-access memory (CRAM)," has emerged to address this fundamental limitation. CRAM performs logic operations directly using the memory cells themselves, without having the data ever leave the memory. The energy and performance benefits of CRAM for both conventional and emerging applications have been well established by prior numerical studies. However, there is a lack of experimental demonstration and study of CRAM to evaluate its computational accuracy, which is a realistic and application-critical metric for its technological feasibility and competitiveness. In this work, a CRAM array based on magnetic tunnel junctions (MTJs) is experimentally demonstrated. First, basic memory operations, as well as 2-, 3-, and 5-input logic operations, are studied. Then, a 1-bit full adder with two different designs is demonstrated. Based on the experimental results, a suite of models has been developed to characterize the accuracy of CRAM computation. Scalar addition, multiplication, and matrix multiplication, which are essential building blocks for many conventional and machine intelligence applications, are evaluated and show promising accuracy performance. With the confirmation of MTJ-based CRAM's accuracy, there is a strong case that this technology will have a significant impact on power- and energy-demanding applications of machine intelligence.

Development of a Natural Language Processing (NLP) model to automatically extract clinical data from electronic health records: results from an Italian comprehensive stroke center.

INTRODUCTION: Data collection often relies on time-consuming manual inputs, with a vast amount of information embedded in unstructured texts such as patients' medical records and clinical notes. Our study aims to develop a pipeline that combines active learning (AL) and NLP techniques to enhance data extraction in an acute ischemic stroke cohort. MATERIALS AND METHODS: Consecutive acute ischemic stroke patients who received reperfusion therapies at IRCCS Humanitas Research Hospital were included. The Italian NLP Bidirectional Encoder Representations from Transformers (BERT) model was trained with AL to automatically extract clinical variables from electronic health text. Simulated active learning performances were evaluated on a set of labels representing patients' comorbidities, comparing Bayesian Uncertainty Sampling by Disagreement (BALD) and random text selection. Prognostic models predicting patients' functional outcomes using Gradient Boosting were trained on manually labelled and semi-automatically extracted data and their performance was compared. RESULTS: The active learning process initially showed null performance until around 20% of texts were labelled, possibly due to root layers freezing in the BERT model, yet overall, active learning improves model learning efficiency across most comorbidities. Prognostic modelling showed no significant difference in performance between models trained on manually labelled versus semi-automatically extracted data, indicating effective prediction capabilities in both settings. CONCLUSIONS: We developed an efficient language model to automate the extraction of clinical data from Italian unstructured health texts in a cohort of ischemic stroke patients. In a preliminary analysis, we demonstrated its potential applicability for enhancing prediction model accuracy.

A multi-timescale synaptic weight based on ferroelectric hafnium zirconium oxide.

Brain-inspired computing emerged as a forefront technology to harness the growing amount of data generated in an increasingly connected society. The complex dynamics involving short- and long-term memory are key to the undisputed performance of biological neural networks. Here, we report on sub-µm-sized artificial synaptic weights exploiting a combination of a ferroelectric space charge effect and oxidation state modulation in the oxide channel of a ferroelectric field effect transistor. They lead to a quasi-continuous resistance tuning of the synapse by a factor of 60 and a fine-grained weight update of more than 200 resistance values. We leverage a fast, saturating ferroelectric effect and a slow, ionic drift and diffusion process to engineer a multi-timescale artificial synapse. Our device demonstrates an endurance of more than 10 10 cycles, a ferroelectric retention of more than 10 years, and various types of volatility behavior on distinct timescales, making it well suited for neuromorphic and cognitive computing.

Resource-efficient fault-tolerant one-way quantum repeater with code concatenation.

One-way quantum repeaters where loss and operational errors are counteracted by quantum error-correcting codes can ensure fast and reliable qubit transmission in quantum networks. It is crucial that the resource requirements of such repeaters, for example, the number of qubits per repeater node and the complexity of the quantum error-correcting operations are kept to a minimum to allow for near-future implementations. To this end, we propose a one-way quantum repeater that targets both the loss and operational error rates in a communication channel in a resource-efficient manner using code concatenation. Specifically, we consider a tree-cluster code as an inner loss-tolerant code concatenated with an outer 5-qubit code for protection against Pauli errors. Adopting flag-based stabilizer measurements, we show that intercontinental distances of up to 10,000 km can be bridged with a minimized resource overhead by interspersing repeater nodes that each specialize in suppressing either loss or operational errors. Our work demonstrates how tailored error-correcting codes can significantly lower the experimental requirements for long-distance quantum communication.

Deep learning-based robust positioning for all-weather autonomous driving.

Interest in autonomous vehicles (AVs) is growing at a rapid pace due to increased convenience, safety benefits and potential environmental gains. Although several leading AV companies predicted that AVs would be on the road by 2020, they are still limited to relatively small-scale trials. The ability to know their precise location on the map is a challenging prerequisite for safe and reliable AVs due to sensor imperfections under adverse environmental and weather conditions, posing a formidable obstacle to their widespread use. Here we propose a deep learning-based self-supervised approach for ego-motion estimation that is a robust and complementary localization solution under inclement weather conditions. The proposed approach is a geometry-aware method that attentively fuses the rich representation capability of visual sensors and the weather-immune features provided by radars using an attention-based learning technique. Our method predicts reliability masks for the sensor measurements, eliminating the deficiencies in the multimodal data. In various experiments we demonstrate the robust all-weather performance and effective cross-domain generalizability under harsh weather conditions such as rain, fog and snow, as well as day and night conditions. Furthermore, we employ a game-theoretic approach to analyse the interpretability of the model predictions, illustrating the independent and uncorrelated failure modes of the multimodal system. We anticipate our work will bring AVs one step closer to safe and reliable all-weather autonomous driving.

Cover runners-up of 2021.

We highlight some of our favorite cover suggestions, submitted by authors last year, that were not ultimately selected for the journal.

Use of temporal contact graphs to understand the evolution of COVID-19 through contact tracing data.

Digital contact tracing has been recently advocated by China and many countries as part of digital prevention measures on COVID-19. Controversies have been raised about their effectiveness in practice as it remains open how they can be fully utilized to control COVID-19. In this article, we show that an abundance of information can be extracted from digital contact tracing for COVID-19 prevention and control. Specifically, we construct a temporal contact graph that quantifies the daily contacts between infectious and susceptible individuals by exploiting a large volume of location-related data contributed by 10,527,737 smartphone users in Wuhan, China. The temporal contact graph reveals five time-varying indicators can accurately capture actual contact trends at population level, demonstrating that travel restrictions (e.g., city lockdown) in Wuhan played an important role in containing COVID-19. We reveal a strong correlation between the contacts level and the epidemic size, and estimate several significant epidemiological parameters (e.g., serial interval). We also show that user participation rate exerts higher influence on situation evaluation than user upload rate does, indicating a sub-sampled dataset would be as good at prediction. At individual level, however, the temporal contact graph plays a limited role, since the behavior distinction between the infected and uninfected individuals are not substantial. The revealed results can tell the effectiveness of digital contact tracing against COVID-19, providing guidelines for governments to implement interventions using information technology.

A general framework for quantifying uncertainty at scale.

In many fields of science, comprehensive and realistic computational models are available nowadays. Often, the respective numerical calculations call for the use of powerful supercomputers, and therefore only a limited number of cases can be investigated explicitly. This prevents straightforward approaches to important tasks like uncertainty quantification and sensitivity analysis. This challenge can be overcome via our recently developed sensitivity-driven dimension-adaptive sparse grid interpolation strategy. The method exploits, via adaptivity, the structure of the underlying model (such as lower intrinsic dimensionality and anisotropic coupling of the uncertain inputs) to enable efficient and accurate uncertainty quantification and sensitivity analysis at scale. Here, we demonstrate the efficiency of this adaptive approach in the context of fusion research, in a realistic, computationally expensive scenario of turbulent transport in a magnetic confinement tokamak device with eight uncertain parameters, reducing the effort by at least two orders of magnitude. In addition, we show that this refinement method intrinsically provides an accurate surrogate model that is nine orders of magnitude cheaper than the high-fidelity model.

Antibodies as programmable, bipedal walkers.

Stochastic modeling of antibody binding dynamics on patterned antigen substrates suggests the separation distance between adjacent antigens could be a control mechanism for the directed bipedal migration of bound antibodies.