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The temperature of surface and epilimnetic waters, closely related to regional air temperatures, responds quickly and directly to climatic changes. As a result, lake surface temperature (LSWT) can be considered an effective indicator of climate change. In this study, we reconstructed and investigated historical and future LSWT across different scenarios for over 80 major lakes in mainland Southeast Asia (SEA), an ecologically diverse region vulnerable to climate impacts. Five different predicting models, incorporating statistical, machine and deep learning approaches, were trained and validated using ERA5 and CHIRPS climatic feature datasets as predictors and 8-day MODIS-derived LSWT from 2000 to 2020 as reference dataset. Best performing model was then applied to predict both historical (1986-2020) and future (2020-2100) LSWT for SEA lakes, utilizing downscaled climatic CORDEX-SEA feature data and multiple Representative Concentration Pathway (RCP). The analysis uncovered historical and future thermal dynamics and long-term trends for both daytime and nighttime LSWT. Among 5 models, XGboost results the most performant (NSE 0.85, RMSE 1.14 °C, MAE 0.69 °C, MBE -0.08 °C) and it has been used for historical reconstruction and future LSWT prediction. The historical analysis revealed a warming trend in SEA lakes, with daytime LSWT increasing at a rate of +0.18 °C/decade and nighttime LSWT at +0.13 °C/decade over the past three decades. These trends appeared of smaller magnitude compared to global estimates of LSWT change rates and less pronounced than concurrent air temperature and LSWT increases in neighbouring regions. Projections under various RCP scenarios indicated continued LSWT warming. Daytime LSWT is projected to increase at varying rates per decade: +0.03 °C under RCP2.6, +0.14 °C under RCP4.5, and +0.29 °C under RCP8.5. Similarly, nighttime LSWT projections under these scenarios are: +0.03 °C, +0.10 °C, and +0.16 °C per decade, respectively. The most optimistic scenario predicted marginal increases of +0.38 °C on average, while the most pessimistic scenario indicated an average LSWT increase of +2.29 °C by end of the century. This study highlights the relevance of LSWT as a climate change indicator in major SEA's freshwater ecosystems. The integration of satellite-derived LSWT, historical and projected climate data into data-driven modelling has enabled new and a more nuanced understanding of LSWT dynamics in relation to climate throughout the entire SEA region.

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BACKGROUND: Tuberculosis (TB) was the leading infectious cause of mortality globally prior to COVID-19 and chest radiography has an important role in the detection, and subsequent diagnosis, of patients with this disease. The conventional experts reading has substantial within- and between-observer variability, indicating poor reliability of human readers. Substantial efforts have been made in utilizing various artificial intelligence-based algorithms to address the limitations of human reading of chest radiographs for diagnosing TB. OBJECTIVE: This systematic literature review (SLR) aims to assess the performance of machine learning (ML) and deep learning (DL) in the detection of TB using chest radiography (chest x-ray [CXR]). METHODS: In conducting and reporting the SLR, we followed the PRISMA (Preferred Reporting Items for Systematic Reviews and Meta-Analyses) guidelines. A total of 309 records were identified from Scopus, PubMed, and IEEE (Institute of Electrical and Electronics Engineers) databases. We independently screened, reviewed, and assessed all available records and included 47 studies that met the inclusion criteria in this SLR. We also performed the risk of bias assessment using Quality Assessment of Diagnostic Accuracy Studies version 2 (QUADAS-2) and meta-analysis of 10 included studies that provided confusion matrix results. RESULTS: Various CXR data sets have been used in the included studies, with 2 of the most popular ones being Montgomery County (n=29) and Shenzhen (n=36) data sets. DL (n=34) was more commonly used than ML (n=7) in the included studies. Most studies used human radiologist's report as the reference standard. Support vector machine (n=5), k-nearest neighbors (n=3), and random forest (n=2) were the most popular ML approaches. Meanwhile, convolutional neural networks were the most commonly used DL techniques, with the 4 most popular applications being ResNet-50 (n=11), VGG-16 (n=8), VGG-19 (n=7), and AlexNet (n=6). Four performance metrics were popularly used, namely, accuracy (n=35), area under the curve (AUC; n=34), sensitivity (n=27), and specificity (n=23). In terms of the performance results, ML showed higher accuracy (mean ~93.71%) and sensitivity (mean ~92.55%), while on average DL models achieved better AUC (mean ~92.12%) and specificity (mean ~91.54%). Based on data from 10 studies that provided confusion matrix results, we estimated the pooled sensitivity and specificity of ML and DL methods to be 0.9857 (95% CI 0.9477-1.00) and 0.9805 (95% CI 0.9255-1.00), respectively. From the risk of bias assessment, 17 studies were regarded as having unclear risks for the reference standard aspect and 6 studies were regarded as having unclear risks for the flow and timing aspect. Only 2 included studies had built applications based on the proposed solutions. CONCLUSIONS: Findings from this SLR confirm the high potential of both ML and DL for TB detection using CXR. Future studies need to pay a close attention on 2 aspects of risk of bias, namely, the reference standard and the flow and timing aspects. TRIAL REGISTRATION: PROSPERO CRD42021277155; https://www.crd.york.ac.uk/prospero/display_record.php?RecordID=277155.

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We discuss the new paradigm of predictive health intelligence, based on the use of modern deep learning algorithms and big biomedical data, along the various dimensions of: a) its potential, b) the limitations it encounters, and c) the sense it makes. We conclude by reasoning on the idea that viewing data as the unique source of sanitary knowledge, fully abstracting from human medical reasoning, may affect the scientific credibility of health predictions.

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Grayscale statistical attributes analysed for 513 extract images taken from pulmonary computed tomography (CT) scan slices of 57 individuals (49 confirmed COVID-19 positive; eight confirmed COVID-19 negative) are able to accurately predict a visual score (VS from 0 to 4) used by a clinician to assess the severity of lung abnormalities in the patients. Some of these attributes can be used graphically to distinguish useful but overlapping distributions for the VS classes. Using machine and deep learning (ML/DL) algorithms with twelve grayscale image attributes as inputs enables the VS classes to be accurately distinguished. A convolutional neural network achieves this with better than 96% accuracy (only 18 images misclassified out of 513) on a supervised learning basis. Analysis of confusion matrices enables the VS prediction performance of ML/DL algorithms to be explored in detail. Those matrices demonstrate that the best performing ML/DL algorithms successfully distinguish between VS classes 0 and 1, which clinicians cannot readily do with the naked eye. Just five image grayscale attributes can also be used to generate an algorithmically defined scoring system (AS) that can also graphically distinguish the degree of pulmonary impacts in the dataset evaluated. The AS classification illustrated involves less overlap between its classes than the VS system and could be exploited as an automated expert system. The best-performing ML/DL models are able to predict the AS classes with better than 99% accuracy using twelve grayscale attributes as inputs. The decision tree and random forest algorithms accomplish that distinction with just one classification error in the 513 images tested.

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The first paradigm of plant breeding involves direct selection-based phenotypic observation, followed by predictive breeding using statistical models for quantitative traits constructed based on genetic experimental design and, more recently, by incorporation of molecular marker genotypes. However, plant performance or phenotype (P) is determined by the combined effects of genotype (G), envirotype (E), and genotype by environment interaction (GEI). Phenotypes can be predicted more precisely by training a model using data collected from multiple sources, including spatiotemporal omics (genomics, phenomics, and enviromics across time and space). Integration of 3D information profiles (G-P-E), each with multidimensionality, provides predictive breeding with both tremendous opportunities and great challenges. Here, we first review innovative technologies for predictive breeding. We then evaluate multidimensional information profiles that can be integrated with a predictive breeding strategy, particularly envirotypic data, which have largely been neglected in data collection and are nearly untouched in model construction. We propose a smart breeding scheme, integrated genomic-enviromic prediction (iGEP), as an extension of genomic prediction, using integrated multiomics information, big data technology, and artificial intelligence (mainly focused on machine and deep learning). We discuss how to implement iGEP, including spatiotemporal models, environmental indices, factorial and spatiotemporal structure of plant breeding data, and cross-species prediction. A strategy is then proposed for prediction-based crop redesign at both the macro (individual, population, and species) and micro (gene, metabolism, and network) scales. Finally, we provide perspectives on translating smart breeding into genetic gain through integrative breeding platforms and open-source breeding initiatives. We call for coordinated efforts in smart breeding through iGEP, institutional partnerships, and innovative technological support.

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BACKGROUND: Rectal cancer is a malignant neoplasm of the large intestine resulting from the uncontrolled proliferation of the rectal tract. Predicting the pathologic response of neoadjuvant chemoradiotherapy at an MRI primary staging scan in patients affected by locally advanced rectal cancer (LARC) could lead to significant improvement in the survival and quality of life of the patients. In this study, the possibility of automatizing this estimation from a primary staging MRI scan, using a fully automated artificial intelligence-based model for the segmentation and consequent characterization of the tumor areas using radiomic features was evaluated. The TRG score was used to evaluate the clinical outcome. METHODS: Forty-three patients under treatment in the IRCCS Sant'Orsola-Malpighi Polyclinic were retrospectively selected for the study; a U-Net model was trained for the automated segmentation of the tumor areas; the radiomic features were collected and used to predict the tumor regression grade (TRG) score. RESULTS: The segmentation of tumor areas outperformed the state-of-the-art results in terms of the Dice score coefficient or was comparable to them but with the advantage of considering mucinous cases. Analysis of the radiomic features extracted from the lesion areas allowed us to predict the TRG score, with the results agreeing with the state-of-the-art results. CONCLUSIONS: The results obtained regarding TRG prediction using the proposed fully automated pipeline prove its possible usage as a viable decision support system for radiologists in clinical practice.

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Phenomics requires quantification of large volumes of image data, necessitating high throughput image processing approaches. Existing image processing pipelines for Drosophila wings, a powerful genetic model for studying the underlying genetics for a broad range of cellular and developmental processes, are limited in speed, precision, and functional versatility. To expand on the utility of the wing as a phenotypic screening system, we developed MAPPER, an automated machine learning-based pipeline that quantifies high-dimensional phenotypic signatures, with each dimension quantifying a unique morphological feature of the Drosophila wing. MAPPER magnifies the power of Drosophila phenomics by rapidly quantifying subtle phenotypic differences in sample populations. We benchmarked MAPPER's accuracy and precision in replicating manual measurements to demonstrate its widespread utility. The morphological features extracted using MAPPER reveal variable sexual dimorphism across Drosophila species and unique underlying sex-specific differences in morphogen signaling in male and female wings. Moreover, the length of the proximal-distal axis across the species and sexes shows a conserved scaling relationship with respect to the wing size. In sum, MAPPER is an open-source tool for rapid, high-dimensional analysis of large imaging datasets. These high-content phenomic capabilities enable rigorous and systematic identification of genotype-to-phenotype relationships in a broad range of screening and drug testing applications and amplify the potential power of multimodal genomic approaches.

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Genome-wide association studies (GWAS) are effectively applied to detect the marker trait associations (MTAs) using whole genome-wide variants for complex quantitative traits in different crop species. GWAS has been applied in wheat for different quality, biotic and abiotic stresses, and agronomic and yield-related traits. Predictions for marker-trait associations are controlled with the development of better statistical models taking population structure and familial relatedness into account. In this review, we have provided a detailed overview of the importance of association mapping, population design, high-throughput genotyping and phenotyping platforms, advancements in statistical models and multiple threshold comparisons, and recent GWA studies conducted in wheat. The information about MTAs utilized for gene characterization and adopted in breeding programs is also provided. In the literature that we surveyed, as many as 86,122 wheat lines have been studied under various GWA studies reporting 46,940 loci. However, further utilization of these is largely limited. The future breakthroughs in area of genomic selection, multi-omics-based approaches, machine, and deep learning models in wheat breeding after exploring the complex genetic structure with the GWAS are also discussed. This is a most comprehensive study of a large number of reports on wheat GWAS and gives a comparison and timeline of technological developments in this area. This will be useful to new researchers or groups who wish to invest in GWAS.

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Background: Left ventricular ejection fraction (LVEF) is the gold standard for evaluating heart failure (HF) in coronary artery disease (CAD) patients. It is an essential metric in categorizing HF patients as preserved (HFpEF), mid-range (HFmEF), and reduced (HFrEF) ejection fraction but differs, depending on whether the ASE/EACVI or ESC guidelines are used to classify HF. Objectives: We sought to investigate the effectiveness of using deep learning as an automated tool to predict LVEF from patient clinical profiles using regression and classification trained models. We further investigate the effect of utilizing other LVEF-based thresholds to examine the discrimination ability of deep learning between HF categories grouped with narrower ranges. Methods: Data from 303 CAD patients were obtained from American and Greek patient databases and categorized based on the American Society of Echocardiography and the European Association of Cardiovascular Imaging (ASE/EACVI) guidelines into HFpEF (EF > 55%), HFmEF (50% ≤ EF ≤ 55%), and HFrEF (EF < 50%). Clinical profiles included 13 demographical and clinical markers grouped as cardiovascular risk factors, medication, and history. The most significant and important markers were determined using linear regression fitting and Chi-squared test combined with a novel dimensionality reduction algorithm based on arc radial visualization (ArcViz). Two deep learning-based models were then developed and trained using convolutional neural networks (CNN) to estimate LVEF levels from the clinical information and for classification into one of three LVEF-based HF categories. Results: A total of seven clinical markers were found important for discriminating between the three HF categories. Using statistical analysis, diabetes, diuretics medication, and prior myocardial infarction were found statistically significant (p < 0.001). Furthermore, age, body mass index (BMI), anti-arrhythmics medication, and previous ventricular tachycardia were found important after projections on the ArcViz convex hull with an average nearest centroid (NC) accuracy of 94%. The regression model estimated LVEF levels successfully with an overall accuracy of 90%, average root mean square error (RMSE) of 4.13, and correlation coefficient of 0.85. A significant improvement was then obtained with the classification model, which predicted HF categories with an accuracy ≥93%, sensitivity ≥89%, 1-specificity <5%, and average area under the receiver operating characteristics curve (AUROC) of 0.98. Conclusions: Our study suggests the potential of implementing deep learning-based models clinically to ensure faster, yet accurate, automatic prediction of HF based on the ASE/EACVI LVEF guidelines with only clinical profiles and corresponding information as input to the models. Invasive, expensive, and time-consuming clinical testing could thus be avoided, enabling reduced stress in patients and simpler triage for further intervention.

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Protein sequences, directly translated from genomic data, need functional and structural annotation. Together with molecular function and biological process, subcellular localization is an important feature necessary for understanding the protein role and the compartment where the mature protein is active. In the case of mitochondrial proteins, their precursor sequences translated by the ribosome machinery include specific patterns from which it is possible not only to recognize their final destination within the organelle but also which of the mitochondrial subcompartments the protein is intended for. Four compartments are routinely discriminated, including the inner and the outer membranes, the intermembrane space, and the matrix. Here we discuss to which extent it is feasible to develop computational methods for detecting mitochondrial targeting peptides in the precursor sequence and to discriminate their final destination in the organelle. We benchmark two of our methods on the general task of recognizing human mitochondrial proteins endowed with an experimentally characterized targeting peptide (TPpred3) and predicting which submitochondrial compartment is the final destination (DeepMito). We describe how to adopt our web servers in order to discriminate which human proteins are endowed with mitochondrial targeting peptides, the position of cleavage sites, and which submitochondrial compartment are intended for. By this, we add some other 1788 human proteins to the 450 ones already manually annotated in UniProt with a mitochondrial targeting peptide, providing for each of them also the characterization of the suborganellar localization.

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Artificial intelligence (AI) in the last decade centered primarily around digitizing and incorporating the large volumes of patient data from electronic health records. AI is now poised to make the next step in health care integration, with precision medicine, imaging support, and development of individual health trends with the popularization of wearable devices. Future clinical pediatric cardiologists will use AI as an adjunct in delivering optimum patient care, with the help of accurate predictive risk calculators, continual health monitoring from wearables, and precision medicine. Physicians must also protect their patients' health information from monetization or exploitation.

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PURPOSE: The purpose of this work is to develop machine and deep learning-based models to predict output and MU based on measured patient quality assurance (QA) data in uniform scanning proton therapy (USPT). METHODS: This study involves 4,231 patient QA measurements conducted over the last 6 years. In the current approach, output and MU are predicted by an empirical model (EM) based on patient treatment plan parameters. In this study, two MATLAB-based machine and deep learning algorithms - Gaussian process regression (GPR) and shallow neural network (SNN) - were developed. The four parameters from patient QA (range, modulation, field size, and measured output factor) were used to train these algorithms. The data were randomized with a training set containing 90% and a testing set containing remaining 10% of the data. The model performance during training was accessed using root mean square error (RMSE) and R-squared values. The trained model was used to predict output based on the three input parameters: range, modulation, and field size. The percent difference was calculated between the predicted and measured output factors. The number of data sets required to make prediction accuracy of GPR and SNN models' invariable was also evaluated. RESULTS: The prediction accuracy of machine and deep learning algorithms is higher than the EM. The output predictions with [GPR, SNN, and EM] within ± 2% and ± 3% difference were [97.16%, 97.64%, and 92.95%] and [99.76%, 99.29%, and 97.18%], respectively. The GPR model outperformed the SNN with a smaller number of training data sets. CONCLUSION: The GPR and SNN models outperformed the EM in terms of prediction accuracy. Machine and deep learning algorithms predicted the output factor and MU for USPT with higher predictive accuracy than EM. In our clinic, these models have been adopted as a secondary check of MU or output factors.

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Data-driven computational approaches have evolved to enable extraction of information from medical images with a reliability, accuracy and speed which is already transforming their interpretation and exploitation in clinical practice. While similar benefits are longed for in the field of interventional imaging, this ambition is challenged by a much higher heterogeneity. Clinical workflows within interventional suites and operating theatres are extremely complex and typically rely on poorly integrated intra-operative devices, sensors, and support infrastructures. Taking stock of some of the most exciting developments in machine learning and artificial intelligence for computer assisted interventions, we highlight the crucial need to take context and human factors into account in order to address these challenges. Contextual artificial intelligence for computer assisted intervention, or CAI4CAI, arises as an emerging opportunity feeding into the broader field of surgical data science. Central challenges being addressed in CAI4CAI include how to integrate the ensemble of prior knowledge and instantaneous sensory information from experts, sensors and actuators; how to create and communicate a faithful and actionable shared representation of the surgery among a mixed human-AI actor team; how to design interventional systems and associated cognitive shared control schemes for online uncertainty-aware collaborative decision making ultimately producing more precise and reliable interventions.

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OBJECTIVE: The purpose of this article is to discuss potential applications of artificial intelligence (AI) in breast imaging and limitations that may slow or prevent its adoption. CONCLUSION: The algorithms of AI for workflow improvement and outcome analyses are advancing. Using imaging data of high quality and quantity, AI can support breast imagers in diagnosis and patient management, but AI cannot yet be relied on or be responsible for physicians' decisions that may affect survival. Education in AI is urgently needed for physicians.

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