Give more data, awareness and control to individual citizens, and they will help COVID-19 containment.

The rapid dynamics of COVID-19 calls for quick and effective tracking of virus transmission chains and early detection of outbreaks, especially in the "phase 2" of the pandemic, when lockdown and other restriction measures are progressively withdrawn, in order to avoid or minimize contagion resurgence. For this purpose, contact-tracing apps are being proposed for large scale adoption by many countries. A centralized approach, where data sensed by the app are all sent to a nation-wide server, raises concerns about citizens' privacy and needlessly strong digital surveillance, thus alerting us to the need to minimize personal data collection and avoiding location tracking. We advocate the conceptual advantage of a decentralized approach, where both contact and location data are collected exclusively in individual citizens' "personal data stores", to be shared separately and selectively (e.g., with a backend system, but possibly also with other citizens), voluntarily, only when the citizen has tested positive for COVID-19, and with a privacy preserving level of granularity. This approach better protects the personal sphere of citizens and affords multiple benefits: it allows for detailed information gathering for infected people in a privacy-preserving fashion; and, in turn this enables both contact tracing, and, the early detection of outbreak hotspots on more finely-granulated geographic scale. The decentralized approach is also scalable to large populations, in that only the data of positive patients need be handled at a central level. Our recommendation is two-fold. First to extend existing decentralized architectures with a light touch, in order to manage the collection of location data locally on the device, and allow the user to share spatio-temporal aggregates-if and when they want and for specific aims-with health authorities, for instance. Second, we favour a longer-term pursuit of realizing a Personal Data Store vision, giving users the opportunity to contribute to collective good in the measure they want, enhancing self-awareness, and cultivating collective efforts for rebuilding society.

Continuous Data-Driven Monitoring in Critical Congenital Heart Disease: Clinical Deterioration Model Development.

BACKGROUND: Critical congenital heart disease (cCHD)-requiring cardiac intervention in the first year of life for survival-occurs globally in 2-3 of every 1000 live births. In the critical perioperative period, intensive multimodal monitoring at a pediatric intensive care unit (PICU) is warranted, as their organs-especially the brain-may be severely injured due to hemodynamic and respiratory events. These 24/7 clinical data streams yield large quantities of high-frequency data, which are challenging in terms of interpretation due to the varying and dynamic physiology innate to cCHD. Through advanced data science algorithms, these dynamic data can be condensed into comprehensible information, reducing the cognitive load on the medical team and providing data-driven monitoring support through automated detection of clinical deterioration, which may facilitate timely intervention. OBJECTIVE: This study aimed to develop a clinical deterioration detection algorithm for PICU patients with cCHD. METHODS: Retrospectively, synchronous per-second data of cerebral regional oxygen saturation (rSO2) and 4 vital parameters (respiratory rate, heart rate, oxygen saturation, and invasive mean blood pressure) in neonates with cCHD admitted to the University Medical Center Utrecht, the Netherlands, between 2002 and 2018 were extracted. Patients were stratified based on mean oxygen saturation during admission to account for physiological differences between acyanotic and cyanotic cCHD. Each subset was used to train our algorithm in classifying data as either stable, unstable, or sensor dysfunction. The algorithm was designed to detect combinations of parameters abnormal to the stratified subpopulation and significant deviations from the patient's unique baseline, which were further analyzed to distinguish clinical improvement from deterioration. Novel data were used for testing, visualized in detail, and internally validated by pediatric intensivists. RESULTS: A retrospective query yielded 4600 hours and 209 hours of per-second data in 78 and 10 neonates for, respectively, training and testing purposes. During testing, stable episodes occurred 153 times, of which 134 (88%) were correctly detected. Unstable episodes were correctly noted in 46 of 57 (81%) observed episodes. Twelve expert-confirmed unstable episodes were missed in testing. Time-percentual accuracy was 93% and 77% for, respectively, stable and unstable episodes. A total of 138 sensorial dysfunctions were detected, of which 130 (94%) were correct. CONCLUSIONS: In this proof-of-concept study, a clinical deterioration detection algorithm was developed and retrospectively evaluated to classify clinical stability and instability, achieving reasonable performance considering the heterogeneous population of neonates with cCHD. Combined analysis of baseline (ie, patient-specific) deviations and simultaneous parameter-shifting (ie, population-specific) proofs would be promising with respect to enhancing applicability to heterogeneous critically ill pediatric populations. After prospective validation, the current-and comparable-models may, in the future, be used in the automated detection of clinical deterioration and eventually provide data-driven monitoring support to the medical team, allowing for timely intervention.

Learning predictive models that use pattern discovery--a bootstrap evaluative approach applied in organ functioning sequences.

An important problem in the Intensive Care is how to predict on a given day of stay the eventual hospital mortality for a specific patient. A recent approach to solve this problem suggested the use of frequent temporal sequences (FTSs) as predictors. Methods following this approach were evaluated in the past by inducing a model from a training set and validating the prognostic performance on an independent test set. Although this evaluative approach addresses the validity of the specific models induced in an experiment, it falls short of evaluating the inductive method itself. To achieve this, one must account for the inherent sources of variation in the experimental design. The main aim of this work is to demonstrate a procedure based on bootstrapping, specifically the .632 bootstrap procedure, for evaluating inductive methods that discover patterns, such as FTSs. A second aim is to apply this approach to find out whether a recently suggested inductive method that discovers FTSs of organ functioning status is superior over a traditional method that does not use temporal sequences when compared on each successive day of stay at the Intensive Care Unit. The use of bootstrapping with logistic regression using pre-specified covariates is known in the statistical literature. Using inductive methods of prognostic models based on temporal sequence discovery within the bootstrap procedure is however novel at least in predictive models in the Intensive Care. Our results of applying the bootstrap-based evaluative procedure demonstrate the superiority of the FTS-based inductive method over the traditional method in terms of discrimination as well as accuracy. In addition we illustrate the insights gained by the analyst into the discovered FTSs from the bootstrap samples.

Combining Supervised and Unsupervised Machine Learning Methods for Phenotypic Functional Genomics Screening.

There has been an increase in the use of machine learning and artificial intelligence (AI) for the analysis of image-based cellular screens. The accuracy of these analyses, however, is greatly dependent on the quality of the training sets used for building the machine learning models. We propose that unsupervised exploratory methods should first be applied to the data set to gain a better insight into the quality of the data. This improves the selection and labeling of data for creating training sets before the application of machine learning. We demonstrate this using a high-content genome-wide small interfering RNA screen. We perform an unsupervised exploratory data analysis to facilitate the identification of four robust phenotypes, which we subsequently use as a training set for building a high-quality random forest machine learning model to differentiate four phenotypes with an accuracy of 91.1% and a kappa of 0.85. Our approach enhanced our ability to extract new knowledge from the screen when compared with the use of unsupervised methods alone.

Data science as a language: challenges for computer science-a position paper.

In this paper, I posit that from a research point of view, Data Science is a language. More precisely Data Science is doing Science using computer science as a language for datafied sciences; much as mathematics is the language of, e.g., physics. From this viewpoint, three (classes) of challenges for computer science are identified; complementing the challenges the closely related Big Data problem already poses to computer science. I discuss the challenges with references to, in my opinion, related, interesting directions in computer science research; note, I claim neither that these directions are the most appropriate to solve the challenges nor that the cited references represent the best work in their field, they are inspirational to me. So, what are these challenges? Firstly, if computer science is to be a language, what should that language look like? While our traditional specifications such as pseudocode are an excellent way to convey what has been done, they fail for more mathematics like reasoning about computations. Secondly, if computer science is to function as a foundation of other, datafied, sciences, its own foundations should be in order. While we have excellent foundations for supervised learning-e.g., by having loss functions to optimize and, more general, by PAC learning (Valiant in Commun ACM 27(11):1134-1142, 1984)-this is far less true for unsupervised learning. Kolmogorov complexity-or, more general, Algorithmic Information Theory-provides a solid base (Li and Vitányi in An introduction to Kolmogorov complexity and its applications, Springer, Berlin, 1993). It provides an objective criterion to choose between competing hypotheses, but it lacks, e.g., an objective measure of the uncertainty of a discovery that datafied sciences need. Thirdly, datafied sciences come with new conceptual challenges. Data-driven scientists come up with data analysis questions that sometimes do and sometimes don't, fit our conceptual toolkit. Clearly, computer science does not suffer from a lack of interesting, deep, research problems. However, the challenges posed by data science point to a large reservoir of untapped problems. Interesting, stimulating problems, not in the least because they are posed by our colleagues in datafied sciences. It is an exciting time to be a computer scientist.

Combination of text-mining algorithms increases the performance.

MOTIVATION: Recently, several information extraction systems have been developed to retrieve relevant information out of biomedical text. However, these methods represent individual efforts. In this paper, we show that by combining different algorithms and their outcome, the results improve significantly. For this reason, CONAN has been created, a system which combines different programs and their outcome. Its methods include tagging of gene/protein names, finding interaction and mutation data, tagging of biological concepts and linking to MeSH and Gene Ontology terms. RESULTS: In this paper, we will present data that show that combining different text-mining algorithms significantly improves the results. Not only is CONAN a full-scale approach that will ultimately cover all of PubMed/MEDLINE, we also show that this universality has no effect on quality: our system performs as well as or better than existing systems. AVAILABILITY: The LDD corpus presented is available by request to the author. The system will be available shortly. For information and updates on CONAN please visit http://www.cs.uu.nl/people/rainer/conan.html.