Interpretation (philosophy)
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Toward understanding the origin and evolution of cellular organisms Open
In this era of high‐throughput biology, bioinformatics has become a major discipline for making sense out of large‐scale datasets. Bioinformatics is usually considered as a practical field developing databases and software tools for suppor…
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ClinVar: improving access to variant interpretations and supporting evidence Open
ClinVar (https://www.ncbi.nlm.nih.gov/clinvar/) is a freely available, public archive of human genetic variants and interpretations of their significance to disease, maintained at the National Institutes of Health. Interpretations of the c…
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Clinical Targets for Continuous Glucose Monitoring Data Interpretation: Recommendations From the International Consensus on Time in Range Open
Improvements in sensor accuracy, greater convenience and ease of use, and expanding reimbursement have led to growing adoption of continuous glucose monitoring (CGM). However, successful utilization of CGM technology in routine clinical pr…
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Evaluating Effect Size in Psychological Research: Sense and Nonsense Open
Effect sizes are underappreciated and often misinterpreted—the most common mistakes being to describe them in ways that are uninformative (e.g., using arbitrary standards) or misleading (e.g., squaring effect-size rs). We propose that effe…
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Modelling and Interpretation of Adsorption Isotherms Open
The need to design low-cost adsorbents for the detoxification of industrial effluents has been a growing concern for most environmental researchers. So modelling of experimental data from adsorption processes is a very important means of p…
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Guidelines for the use and interpretation of assays for monitoring autophagy (4th edition)<sup>1</sup> Open
In 2008, we published the first set of guidelines for standardizing research in autophagy. Since then, this topic has received increasing attention, and many scientists have entered the field. Our knowledge base and relevant new technologi…
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Age of Surveillance Capitalism – The Fight for a Human Future at the New Frontier of Power. Open
As an educator have you recently heard the term or perhaps even been told to be data driven? Inherent in this simple two-word statement is a quagmire of ethical and privacy concerns that educators must confront to reach the goal and realiz…
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GPT-3: Its Nature, Scope, Limits, and Consequences Open
In this commentary, we discuss the nature of reversible and irreversible questions, that is, questions that may enable one to identify the nature of the source of their answers. We then introduce GPT-3, a third-generation, autoregressive l…
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Equality of Opportunity in Supervised Learning Open
We propose a criterion for discrimination against a specified sensitive attribute in supervised learning, where the goal is to predict some target based on available features. Assuming data about the predictor, target, and membership in th…
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Definitions, methods, and applications in interpretable machine learning Open
Significance The recent surge in interpretability research has led to confusion on numerous fronts. In particular, it is unclear what it means to be interpretable and how to select, evaluate, or even discuss methods for producing interpret…
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Receiver operating characteristic curve: overview and practical use for clinicians Open
Using diagnostic testing to determine the presence or absence of a disease is essential in clinical practice. In many cases, test results are obtained as continuous values and require a process of conversion and interpretation and into a d…
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Variant Review with the Integrative Genomics Viewer Open
Manual review of aligned reads for confirmation and interpretation of variant calls is an important step in many variant calling pipelines for next-generation sequencing (NGS) data. Visual inspection can greatly increase the confidence in …
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Explaining Deep Neural Networks and Beyond: A Review of Methods and Applications Open
With the broader and highly successful usage of machine learning in industry\nand the sciences, there has been a growing demand for Explainable AI.\nInterpretability and explanation methods for gaining a better understanding\nabout the pro…
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Citations, Citation Indicators, and Research Quality: An Overview of Basic Concepts and Theories Open
Citations are increasingly used as performance indicators in research policy and within the research system. Usually, citations are assumed to reflect the impact of the research or its quality. What is the justification for these assumptio…
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Systematic and collaborative approach to problem solving using X-ray photoelectron spectroscopy Open
The methodology presented within this work is a result of years of interactions between many junior and senior X-ray Photoelectron Spectroscopy (XPS) users operating within the CasaXPS spectral processing and interpretation program framewo…
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Studying configurations with qualitative comparative analysis: Best practices in strategy and organization research Open
Qualitative comparative analysis is increasingly applied in strategy and organization research. The main purpose of our essay is to support this growing community of qualitative comparative analysis scholars by identifying best practices t…
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The Minimum Inhibitory Concentration of Antibiotics: Methods, Interpretation, Clinical Relevance Open
Inefficiency of medical therapies used in order to cure patients with bacterial infections requires not only to actively look for new therapeutic strategies but also to carefully select antibiotics based on variety of parameters, including…
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A Basic Guide to Real Time PCR in Microbial Diagnostics: Definitions, Parameters, and Everything Open
Real time PCR (quantitative PCR, qPCR) is now a well-established method for the detection, quantification, and typing of different microbial agents in the areas of clinical and veterinary diagnostics and food safety. Although the concept o…
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Interpretation and evolution of open-circuit voltage, recombination, ideality factor and subgap defect states during reversible light-soaking and irreversible degradation of perovskite solar cells Open
Insights into the interplay of different recombination mechanisms and their origins (bulk, surface) are provided comparing fresh, light-soaked and aged devices.
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Extracting spatial effects from machine learning model using local interpretation method: An example of SHAP and XGBoost Open
Machine learning and artificial intelligence (ML/AI), previously considered black box approaches, are becoming more interpretable, as a result of the recent advances in eXplainable AI (XAI). In particular, local interpretation methods such…
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On the use of deep learning for computational imaging Open
Since their inception in the 1930–1960s, the research disciplines of computational imaging and machine learning have followed parallel tracks and, during the last two decades, experienced explosive growth drawing on similar progress in mat…
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Interpretability Beyond Feature Attribution: Quantitative Testing with\n Concept Activation Vectors (TCAV) Open
The interpretation of deep learning models is a challenge due to their size,\ncomplexity, and often opaque internal state. In addition, many systems, such as\nimage classifiers, operate on low-level features rather than high-level\nconcept…
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Ordinal Regression Models in Psychology: A Tutorial Open
Ordinal variables, although extremely common in psychology, are almost exclusively analyzed with statistical models that falsely assume them to be metric. This practice can lead to distorted effect-size estimates, inflated error rates, and…
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Interpretation of Neural Networks Is Fragile Open
In order for machine learning to be trusted in many applications, it is critical to be able to reliably explain why the machine learning algorithm makes certain predictions. For this reason, a variety of methods have been developed recentl…
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Residual Networks Behave Like Ensembles of Relatively Shallow Networks Open
In this work we propose a novel interpretation of residual networks showing that they can be seen as a collection of many paths of differing length. Moreover, residual networks seem to enable very deep networks by leveraging only the short…
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Effect size measures for multilevel models: definition, interpretation, and TIMSS example Open
Effect size reporting is crucial for interpretation of applied research results and for conducting meta-analysis. However, clear guidelines for reporting effect size in multilevel models have not been provided. This report suggests and dem…
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PlotsOfData—A web app for visualizing data together with their summaries Open
Reporting of the actual data in graphs and plots increases transparency and enables independent evaluation. On the other hand, data summaries are often used in graphs because they aid interpretation. To democratize state-of-the-art data vi…
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SynergyFinder Plus: Toward Better Interpretation and Annotation of Drug Combination Screening Datasets Open
Combinatorial therapies have been recently proposed to improve the efficacy of anticancer treatment. The SynergyFinder R package is a software used to analyze pre-clinical drug combination datasets. Here, we report the major updates to the…
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The C-Word: Scientific Euphemisms Do Not Improve Causal Inference From Observational Data Open
Causal inference is a core task of science. However, authors and editors often refrain from explicitly acknowledging the causal goal of research projects; they refer to causal effect estimates as associational estimates. This commentary ar…
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HIPPIE v2.0: enhancing meaningfulness and reliability of protein–protein interaction networks Open
The increasing number of experimentally detected interactions between proteins makes it difficult for researchers to extract the interactions relevant for specific biological processes or diseases. This makes it necessary to accompany the …