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Objective:
Hypertension has long been recognized as one of the most important predisposing factors for cardiovascular diseases and mortality.
In recent years, machine learning methods have shown potential in diagnostic and predictive approaches in chronic diseases.
Electronic health records (EHRs) have emerged as a reliable source of longitudinal data. The aim of this study is to predict the onset of hypertension using modern deep learning (DL) architectures, specifically long short-term memory (LSTM) networks, and longitudinal EHRs.
Materials and Methods:
We compare this approach to the best performing models reported from previous works, particularly XGboost, applied to aggregated features.
Our work is based on data from 233 895 adult patients from a large health system in the United States. We divided our population into 2 distinct longitudinal datasets based on the diagnosis date.
To ensure generalization to unseen data, we trained our models on the first dataset (dataset A "train and validation") using cross-validation, and then applied the models to a second dataset (dataset B "test") to assess their performance.
We also experimented with 2 different time-windows before the onset of hypertension and evaluated the impact on model performance.
Results:
With the LSTM network, we were able to achieve an area under the receiver operating characteristic curve value of 0.98 in the "train and validation" dataset A and 0.94 in the "test" dataset B for a prediction time window of 1 year. Lipid disorders, type 2 diabetes, and renal disorders are found to be associated with incident hypertension.
Conclusion:
These findings show that DL models based on temporal EHR data can improve the identification of patients at high risk of hypertension and corresponding driving factors. In the long term, this work may support identifying individuals who are at high risk for developing hypertension and facilitate earlier intervention to prevent the future development of hypertension.
We present the extension of the Kalmag model, proposed as a candidate for IGRF-13, to the twentieth century.
The dataset serving its derivation has been complemented by new measurements coming from satellites, ground-based observatories and land, marine and airborne surveys.
As its predecessor, this version is derived from a combination of a Kalman filter and a smoothing algorithm, providing mean models and associated uncertainties. These quantities permit a precise estimation of locations where mean solutions can be considered as reliable or not.
The temporal resolution of the core field and the secular variation was set to 0.1 year over the 122 years the model is spanning.
Nevertheless, it can be shown through ensembles a posteriori sampled, that this resolution can be effectively achieved only by a limited amount of spatial scales and during certain time periods.
Unsurprisingly, highest accuracy in both space and time of the core field and the secular variation is achieved during the CHAMP and Swarm era. In this version of Kalmag, a particular effort was made for resolving the small-scale lithospheric field.
Under specific statistical assumptions, the latter was modeled up to spherical harmonic degree and order 1000, and signal from both satellite and survey measurements contributed to its development.
External and induced fields were jointly estimated with the rest of the model. We show that their large scales could be accurately extracted from direct measurements whenever the latter exhibit a sufficiently high temporal coverage.
Temporally resolving these fields down to 3 hours during the CHAMP and Swarm missions, gave us access to the link between induced and magnetospheric fields. In particular, the period dependence of the driving signal on the induced one could be directly observed.
The model is available through various physical and statistical quantities on a dedicated website at https://ionocovar.agnld.uni-potsdam.de/Kalmag/.
Simple Summary Gliomas are heterogenous types of cancer, therefore the therapy should be personalized and targeted toward specific pathways. We developed a methodology that corrected strong batch effects from The Cancer Genome Atlas datasets and estimated glioma grade-specific co-enrichment mechanisms using machine learning. Our findings created hypotheses for annotations, e.g., pathways, that should be considered as therapeutic targets. Gliomas develop and grow in the brain and central nervous system. Examining glioma grading processes is valuable for improving therapeutic challenges. One of the most extensive repositories storing transcriptomics data for gliomas is The Cancer Genome Atlas (TCGA). However, such big cohorts should be processed with caution and evaluated thoroughly as they can contain batch and other effects. Furthermore, biological mechanisms of cancer contain interactions among biomarkers. Thus, we applied an interpretable machine learning approach to discover such relationships. This type of transparent learning provides not only good predictability, but also reveals co-predictive mechanisms among features. In this study, we corrected the strong and confounded batch effect in the TCGA glioma data. We further used the corrected datasets to perform comprehensive machine learning analysis applied on single-sample gene set enrichment scores using collections from the Molecular Signature Database. Furthermore, using rule-based classifiers, we displayed networks of co-enrichment related to glioma grades. Moreover, we validated our results using the external glioma cohorts. We believe that utilizing corrected glioma cohorts from TCGA may improve the application and validation of any future studies. Finally, the co-enrichment and survival analysis provided detailed explanations for glioma progression and consequently, it should support the targeted treatment.
Shams et al. report that glioma patients' motor status is predicted accurately by diffusion MRI metrics along the corticospinal tract based on support vector machine method, reaching an overall accuracy of 77%. They show that these metrics are more effective than demographic and clinical variables.
Along tract statistics enables white matter characterization using various diffusion MRI metrics. These diffusion models reveal detailed insights into white matter microstructural changes with development, pathology and function. Here, we aim at assessing the clinical utility of diffusion MRI metrics along the corticospinal tract, investigating whether motor glioma patients can be classified with respect to their motor status. We retrospectively included 116 brain tumour patients suffering from either left or right supratentorial, unilateral World Health Organization Grades II, III and IV gliomas with a mean age of 53.51 +/- 16.32 years. Around 37% of patients presented with preoperative motor function deficits according to the Medical Research Council scale. At group level comparison, the highest non-overlapping diffusion MRI differences were detected in the superior portion of the tracts' profiles. Fractional anisotropy and fibre density decrease, apparent diffusion coefficient axial diffusivity and radial diffusivity increase. To predict motor deficits, we developed a method based on a support vector machine using histogram-based features of diffusion MRI tract profiles (e.g. mean, standard deviation, kurtosis and skewness), following a recursive feature elimination method. Our model achieved high performance (74% sensitivity, 75% specificity, 74% overall accuracy and 77% area under the curve). We found that apparent diffusion coefficient, fractional anisotropy and radial diffusivity contributed more than other features to the model. Incorporating the patient demographics and clinical features such as age, tumour World Health Organization grade, tumour location, gender and resting motor threshold did not affect the model's performance, revealing that these features were not as effective as microstructural measures. These results shed light on the potential patterns of tumour-related microstructural white matter changes in the prediction of functional deficits.
Psychology and nutritional science research has highlighted the impact of negative emotions and cognitive load on calorie consumption behaviour using subjective questionnaires. Isolated studies in other domains objectively assess cognitive load without considering its effects on eating behaviour. This study aims to explore the potential for developing an integrated eating behaviour assistant system that incorporates cognitive load factors. Two experimental sessions were conducted using custom-developed experimentation software to induce different stimuli. During these sessions, we collected 30 h of physiological, food consumption, and affective states questionnaires data to automatically detect cognitive load and analyse its effect on food choice. Utilising grid search optimisation and leave-one-subject-out cross-validation, a support vector machine model achieved a mean classification accuracy of 85.12% for the two cognitive load tasks using eight relevant features. Statistical analysis was performed on calorie consumption and questionnaire data. Furthermore, 75% of the subjects with higher negative affect significantly increased consumption of specific foods after high-cognitive-load tasks. These findings offer insights into the intricate relationship between cognitive load, affective states, and food choice, paving the way for an eating behaviour assistant system to manage food choices during cognitive load. Future research should enhance system capabilities and explore real-world applications.
The ZuCo benchmark on cross-subject reading task classification with EEG and eye-tracking data
(2023)
We present a new machine learning benchmark for reading task classification with the goal of advancing EEG and eye-tracking research at the intersection between computational language processing and cognitive neuroscience. The benchmark task consists of a cross-subject classification to distinguish between two reading paradigms: normal reading and task-specific reading. The data for the benchmark is based on the Zurich Cognitive Language Processing Corpus (ZuCo 2.0), which provides simultaneous eye-tracking and EEG signals from natural reading of English sentences. The training dataset is publicly available, and we present a newly recorded hidden testset. We provide multiple solid baseline methods for this task and discuss future improvements. We release our code and provide an easy-to-use interface to evaluate new approaches with an accompanying public leaderboard: .
In the context of persistent images of self-perpetuated technologies, we discuss the interplay of digital technologies and organisational dynamics against the backdrop of systems theory. Building on the case of an international corporation that, during an agile reorganisation, introduced an AI-based personnel management platform, we show how technical systems produce a form of algorithmic contingency that subsequently leads to the emergence of formal and informal interaction systems. Using the concept of datafication, we explain how these interactions are barriers to the self-perpetuation of data-based decision-making, making it possible to take into consideration further decision factors and complementing the output of the platform. The research was carried out within the scope of the research project ‘Organisational Implications of Digitalisation: The Development of (Post-)Bureaucratic Organisational Structures in the Context of Digital Transformation’ funded by the German Research Foundation (DFG).
Pathogens and animal pests (P&A) are a major threat to global food security as they directly affect the quantity and quality of food. The Southern Amazon, Brazil's largest domestic region for soybean, maize and cotton production, is particularly vulnerable to the outbreak of P&A due to its (sub)tropical climate and intensive farming systems. However, little is known about the spatial distribution of P&A and the related yield losses. Machine learning approaches for the automated recognition of plant diseases can help to overcome this research gap. The main objectives of this study are to (1) evaluate the performance of Convolutional Neural Networks (ConvNets) in classifying P&A, (2) map the spatial distribution of P&A in the Southern Amazon, and (3) quantify perceived yield and economic losses for the main soybean and maize P&A. The objectives were addressed by making use of data collected with the smartphone application Plantix. The core of the app's functioning is the automated recognition of plant diseases via ConvNets. Data on expected yield losses were gathered through a short survey included in an "expert" version of the application, which was distributed among agronomists. Between 2016 and 2020, Plantix users collected approximately 78,000 georeferenced P&A images in the Southern Amazon. The study results indicate a high performance of the trained ConvNets in classifying 420 different crop-disease combinations. Spatial distribution maps and expert-based yield loss estimates indicate that maize rust, bacterial stalk rot and the fall armyworm are among the most severe maize P&A, whereas soybean is mainly affected by P&A like anthracnose, downy mildew, frogeye leaf spot, stink bugs and brown spot. Perceived soybean and maize yield losses amount to 12 and 16%, respectively, resulting in annual yield losses of approximately 3.75 million tonnes for each crop and economic losses of US$2 billion for both crops together. The high level of accuracy of the trained ConvNets, when paired with widespread use from following a citizen-science approach, results in a data source that will shed new light on yield loss estimates, e.g., for the analysis of yield gaps and the development of measures to minimise them.
A review of source models to further the understanding of the seismicity of the Groningen field
(2022)
The occurrence of felt earthquakes due to gas production in Groningen has initiated numerous studies and model attempts to understand and quantify induced seismicity in this region. The whole bandwidth of available models spans the range from fully deterministic models to purely empirical and stochastic models. In this article, we summarise the most important model approaches, describing their main achievements and limitations. In addition, we discuss remaining open questions and potential future directions of development.
PyFin-sentiment
(2023)
Responding to the poor performance of generic automated sentiment analysis solutions on domain-specific texts, we collect a dataset of 10,000 tweets discussing the topics of finance and investing. We manually assign each tweet its market sentiment, i.e., the investor’s anticipation of a stock’s future return. Using this data, we show that all existing sentiment models trained on adjacent domains struggle with accurate market sentiment analysis due to the task’s specialized vocabulary. Consequently, we design, train, and deploy our own sentiment model. It outperforms all previous models (VADER, NTUSD-Fin, FinBERT, TwitterRoBERTa) when evaluated on Twitter posts. On posts from a different platform, our model performs on par with BERT-based large language models. We achieve this result at a fraction of the training and inference costs due to the model’s simple design. We publish the artifact as a python library to facilitate its use by future researchers and practitioners.
Averting today's loss of biodiversity and ecosystem services can be achieved through conservation efforts, especially of keystone species. Giraffes (Giraffa camelopardalis) play an important role in sustaining Africa's ecosystems, but are 'vulnerable' according to the IUCN Red List since 2016. Monitoring an animal's behavior in the wild helps to develop and assess their conservation management. One mechanism for remote tracking of wildlife behavior is to attach accelerometers to animals to record their body movement. We tested two different commercially available high-resolution accelerometers, e-obs and Africa Wildlife Tracking (AWT), attached to the top of the heads of three captive giraffes and analyzed the accuracy of automatic behavior classifications, focused on the Random Forests algorithm. For both accelerometers, behaviors of lower variety in head and neck movements could be better predicted (i.e., feeding above eye level, mean prediction accuracy e-obs/AWT: 97.6%/99.7%; drinking: 96.7%/97.0%) than those with a higher variety of body postures (such as standing: 90.7-91.0%/75.2-76.7%; rumination: 89.6-91.6%/53.5-86.5%). Nonetheless both devices come with limitations and especially the AWT needs technological adaptations before applying it on animals in the wild. Nevertheless, looking at the prediction results, both are promising accelerometers for behavioral classification of giraffes. Therefore, these devices when applied to free-ranging animals, in combination with GPS tracking, can contribute greatly to the conservation of giraffes.
Background:
COVID-19 has infected millions of people worldwide and is responsible for several hundred thousand fatalities. The COVID-19 pandemic has necessitated thoughtful resource allocation and early identification of high-risk patients. However, effective methods to meet these needs are lacking.
Objective:
The aims of this study were to analyze the electronic health records (EHRs) of patients who tested positive for COVID-19 and were admitted to hospitals in the Mount Sinai Health System in New York City; to develop machine learning models for making predictions about the hospital course of the patients over clinically meaningful time horizons based on patient characteristics at admission; and to assess the performance of these models at multiple hospitals and time points.
Methods:
We used Extreme Gradient Boosting (XGBoost) and baseline comparator models to predict in-hospital mortality and critical events at time windows of 3, 5, 7, and 10 days from admission. Our study population included harmonized EHR data from five hospitals in New York City for 4098 COVID-19-positive patients admitted from March 15 to May 22, 2020. The models were first trained on patients from a single hospital (n=1514) before or on May 1, externally validated on patients from four other hospitals (n=2201) before or on May 1, and prospectively validated on all patients after May 1 (n=383). Finally, we established model interpretability to identify and rank variables that drive model predictions.
Results:
Upon cross-validation, the XGBoost classifier outperformed baseline models, with an area under the receiver operating characteristic curve (AUC-ROC) for mortality of 0.89 at 3 days, 0.85 at 5 and 7 days, and 0.84 at 10 days. XGBoost also performed well for critical event prediction, with an AUC-ROC of 0.80 at 3 days, 0.79 at 5 days, 0.80 at 7 days, and 0.81 at 10 days. In external validation, XGBoost achieved an AUC-ROC of 0.88 at 3 days, 0.86 at 5 days, 0.86 at 7 days, and 0.84 at 10 days for mortality prediction. Similarly, the unimputed XGBoost model achieved an AUC-ROC of 0.78 at 3 days, 0.79 at 5 days, 0.80 at 7 days, and 0.81 at 10 days. Trends in performance on prospective validation sets were similar. At 7 days, acute kidney injury on admission, elevated LDH, tachypnea, and hyperglycemia were the strongest drivers of critical event prediction, while higher age, anion gap, and C-reactive protein were the strongest drivers of mortality prediction.
Conclusions:
We externally and prospectively trained and validated machine learning models for mortality and critical events for patients with COVID-19 at different time horizons. These models identified at-risk patients and uncovered underlying relationships that predicted outcomes.
On 21 April 2021, the European Commission presented its long-awaited proposal for a Regulation “laying down harmonized rules on Artificial Intelligence”, the so-called “Artificial Intelligence Act” (AIA). This article takes a critical look at the proposed regulation. After an introduction (1), the paper analyzes the unclear preemptive effect of the AIA and EU competences (2), the scope of application (3), the prohibited uses of Artificial Intelligence (AI) (4), the provisions on high-risk AI systems (5), the obligations of providers and users (6), the requirements for AI systems with limited risks (7), the enforcement system (8), the relationship of the AIA with the existing legal framework (9), and the regulatory gaps (10). The last section draws some final conclusions (11).
Polygenic risk scores (PRS) aggregating results from genome-wide association studies are the state of the art in the prediction of susceptibility to complex traits or diseases, yet their predictive performance is limited for various reasons, not least of which is their failure to incorporate the effects of gene-gene interactions. Novel machine learning algorithms that use large amounts of data promise to find gene-gene interactions in order to build models with better predictive performance than PRS. Here, we present a data preprocessing step by using data-mining of contextual information to reduce the number of features, enabling machine learning algorithms to identify gene-gene interactions. We applied our approach to the Parkinson's Progression Markers Initiative (PPMI) dataset, an observational clinical study of 471 genotyped subjects (368 cases and 152 controls). With an AUC of 0.85 (95% CI = [0.72; 0.96]), the interaction-based prediction model outperforms the PRS (AUC of 0.58 (95% CI = [0.42; 0.81])). Furthermore, feature importance analysis of the model provided insights into the mechanism of Parkinson's disease. For instance, the model revealed an interaction of previously described drug target candidate genes TMEM175 and GAPDHP25. These results demonstrate that interaction-based machine learning models can improve genetic prediction models and might provide an answer to the missing heritability problem.
There is no consensus on which statistical model estimates school value-added (VA) most accurately. To date, the two most common statistical models used for the calculation of VA scores are two classical methods: linear regression and multilevel models. These models have the advantage of being relatively transparent and thus understandable for most researchers and practitioners. However, these statistical models are bound to certain assumptions (e.g., linearity) that might limit their prediction accuracy. Machine learning methods, which have yielded spectacular results in numerous fields, may be a valuable alternative to these classical models. Although big data is not new in general, it is relatively new in the realm of social sciences and education. New types of data require new data analytical approaches. Such techniques have already evolved in fields with a long tradition in crunching big data (e.g., gene technology). The objective of the present paper is to competently apply these "imported" techniques to education data, more precisely VA scores, and assess when and how they can extend or replace the classical psychometrics toolbox. The different models include linear and non-linear methods and extend classical models with the most commonly used machine learning methods (i.e., random forest, neural networks, support vector machines, and boosting). We used representative data of 3,026 students in 153 schools who took part in the standardized achievement tests of the Luxembourg School Monitoring Program in grades 1 and 3. Multilevel models outperformed classical linear and polynomial regressions, as well as different machine learning models. However, it could be observed that across all schools, school VA scores from different model types correlated highly. Yet, the percentage of disagreements as compared to multilevel models was not trivial and real-life implications for individual schools may still be dramatic depending on the model type used. Implications of these results and possible ethical concerns regarding the use of machine learning methods for decision-making in education are discussed.
The radiation belts of the Earth, filled with energetic electrons, comprise complex and dynamic systems that pose a significant threat to satellite operation. While various models of electron flux both for low and relativistic energies have been developed, the behavior of medium energy (120-600 keV) electrons, especially in the MEO region, remains poorly quantified. At these energies, electrons are driven by both convective and diffusive transport, and their prediction usually requires sophisticated 4D modeling codes. In this paper, we present an alternative approach using the Light Gradient Boosting (LightGBM) machine learning algorithm. The Medium Energy electRon fLux In Earth's outer radiatioN belt (MERLIN) model takes as input the satellite position, a combination of geomagnetic indices and solar wind parameters including the time history of velocity, and does not use persistence. MERLIN is trained on >15 years of the GPS electron flux data and tested on more than 1.5 years of measurements. Tenfold cross validation yields that the model predicts the MEO radiation environment well, both in terms of dynamics and amplitudes o f flux. Evaluation on the test set shows high correlation between the predicted and observed electron flux (0.8) and low values of absolute error. The MERLIN model can have wide space weather applications, providing information for the scientific community in the form of radiation belts reconstructions, as well as industry for satellite mission design, nowcast of the MEO environment, and surface charging analysis.
The nematode Caenorhabditis elegans (C. elegans) is often used as an alternative animal model due to several advantages such as morphological changes that can be seen directly under a microscope. Limitations of the model include the usage of expensive and cumbersome microscopes, and restrictions of the comprehensive use of C. elegans for toxicological trials. With the general applicability of the detection of C. elegans from microscope images via machine learning, as well as of smartphone-based microscopes, this article investigates the suitability of smartphone-based microscopy to detect C. elegans in a complete Petri dish. Thereby, the article introduces a smartphone-based microscope (including optics, lighting, and housing) for monitoring C. elegans and the corresponding classification via a trained Histogram of Oriented Gradients (HOG) feature-based Support Vector Machine for the automatic detection of C. elegans. Evaluation showed classification sensitivity of 0.90 and specificity of 0.85, and thereby confirms the general practicability of the chosen approach.
During the last few decades, the rapid separation of the Small Aral Sea from the isolated basin has changed its hydrological and ecological conditions tremendously. In the present study, we developed and validated the hybrid model for the Syr Darya River basin based on a combination of state-of-the-art hydrological and machine learning models. Climate change impact on freshwater inflow into the Small Aral Sea for the projection period 2007-2099 has been quantified based on the developed hybrid model and bias corrected and downscaled meteorological projections simulated by four General Circulation Models (GCM) for each of three Representative Concentration Pathway scenarios (RCP). The developed hybrid model reliably simulates freshwater inflow for the historical period with a Nash-Sutcliffe efficiency of 0.72 and a Kling-Gupta efficiency of 0.77. Results of the climate change impact assessment showed that the freshwater inflow projections produced by different GCMs are misleading by providing contradictory results for the projection period. However, we identified that the relative runoff changes are expected to be more pronounced in the case of more aggressive RCP scenarios. The simulated projections of freshwater inflow provide a basis for further assessment of climate change impacts on hydrological and ecological conditions of the Small Aral Sea in the 21st Century.
The selection of a nest site is crucial for successful reproduction of birds. Animals which re-use or occupy nest sites constructed by other species often have limited choice. Little is known about the criteria of nest-stealing species to choose suitable nesting sites and habitats. Here, we analyze breeding-site selection of an obligatory "nest-cleptoparasite", the Amur Falcon Falco amurensis. We collected data on nest sites at Muraviovka Park in the Russian Far East, where the species breeds exclusively in nests of the Eurasian Magpie Pica pica. We sampled 117 Eurasian Magpie nests, 38 of which were occupied by Amur Falcons. Nest-specific variables were assessed, and a recently developed habitat classification map was used to derive landscape metrics. We found that Amur Falcons chose a wide range of nesting sites, but significantly preferred nests with a domed roof. Breeding pairs of Eurasian Hobby Falco subbuteo and Eurasian Magpie were often found to breed near the nest in about the same distance as neighboring Amur Falcon pairs. Additionally, the occurrence of the species was positively associated with bare soil cover, forest cover, and shrub patches within their home range and negatively with the distance to wetlands. Areas of wetlands and fallow land might be used for foraging since Amur Falcons mostly depend on an insect diet. Additionally, we found that rarely burned habitats were preferred. Overall, the effect of landscape variables on the choice of actual nest sites appeared to be rather small. We used different classification methods to predict the probability of occurrence, of which the Random forest method showed the highest accuracy. The areas determined as suitable habitat showed a high concordance with the actual nest locations. We conclude that Amur Falcons prefer to occupy newly built (domed) nests to ensure high nest quality, as well as nests surrounded by available feeding habitats.