BackgroundWhile there are many methods for predicting protein-protein interaction, very few can determine the specific site of interaction on each protein. Characterization of the specific sequence regions mediating interaction (binding sites) is crucial for an understanding of cellular pathways. Experimental methods often report false binding sites due to experimental limitations, while computational methods tend to require data which is not available at the proteome-scale. Here we present PIPE-Sites, a novel method of protein specific binding site prediction based on pairs of re-occurring polypeptide sequences, which have been previously shown to accurately predict protein-protein interactions. PIPE-Sites operates at high specificity and requires only the sequences of query proteins and a database of known binary interactions with no binding site data, making it applicable to binding site prediction at the proteome-scale.ResultsPIPE-Sites was evaluated using a dataset of 265 yeast and 423 human interacting proteins pairs with experimentally-determined binding sites. We found that PIPE-Sites predictions were closer to the confirmed binding site than those of two existing binding site prediction methods based on domain-domain interactions, when applied to the same dataset. Finally, we applied PIPE-Sites to two datasets of 2347 yeast and 14,438 human novel interacting protein pairs predicted to interact with high confidence. An analysis of the predicted interaction sites revealed a number of protein subsequences which are highly re-occurring in binding sites and which may represent novel binding motifs.ConclusionsPIPE-Sites is an accurate method for predicting protein binding sites and is applicable to the proteome-scale. Thus, PIPE-Sites could be useful for exhaustive analysis of protein binding patterns in whole proteomes as well as discovery of novel binding motifs. PIPE-Sites is available online at http://pipe-sites.cgmlab.org/.
Anticipatory thinking is a critical cognitive skill for successfully navigating complex, ambiguous systems in which individuals must analyze system states, anticipate outcomes, and forecast future events. For example, in military planning, intelligence analysis, business, medicine, and social services, individuals must use information to identify warnings, anticipate a spectrum of possible outcomes, and forecast likely futures in order to avoid tactical and strategic surprise. Existing methods for examining anticipatory thinking skill have relied upon task-specific behavioral measures or are resource-intensive, both of which are challenging to scale. Given the increasing importance of anticipatory thinking in many domains, developing a generic assessment of this skill and identifying the underlying cognitive mechanisms supporting it are paramount. The work reported here focuses on the development and validation of the anticipatory thinking assessment (ANTA) for measuring the divergent generative process of anticipatory thinking. Two-hundred and ten participants completed the ANTA, which required them to anticipate possible risks, opportunities, trends, or other uncertainties associated with a focal topic. Responses to the anticipatory thinking and divergent thinking tasks were rated by trained raters on a five-point scale according to the uniqueness, specificity, and remoteness of responses. Results supported the ANTA's construct validity, convergent validity, and discriminant validity. We also explored the relationship between the ANTA scores and certain psychological traits and cognitive measures (need for cognition, need for closure, and mindfulness). Our findings suggest that the ANTA is a psychometrically valid instrument that may help researchers investigate anticipatory thinking in new contexts.
Objectives The objectives of this study were to test in real time a Trauma Triage, Treatment, and Training Decision Support (4TDS) machine learning (ML) model of shock detection in a prospective silent trial, and to evaluate specificity, sensitivity, and other estimates of diagnostic performance compared to the gold standard of electronic medical records (EMRs) review. Design We performed a single-center diagnostic performance study. Patients and setting A prospective cohort consisted of consecutive patients aged 18 years and older who were admitted from May 1 through September 30, 2020 to six Mayo Clinic intensive care units (ICUs) and five progressive care units. Measurements and main results During the study time, 5,384 out of 6,630 hospital admissions were eligible. During the same period, the 4TDS shock model sent 825 alerts and 632 were eligible. Among 632 hospital admissions with alerts, 287 were screened positive and 345 were negative. Among 4,752 hospital admissions without alerts, 78 were screened positive and 4,674 were negative. The area under the receiver operating characteristics curve for the 4TDS shock model was 0.86 (95% CI 0.85-0.87%). The 4TDS shock model demonstrated a sensitivity of 78.6% (95% CI 74.1-82.7%) and a specificity of 93.1% (95% CI 92.4-93.8%). The model showed a positive predictive value of 45.4% (95% CI 42.6-48.3%) and a negative predictive value of 98.4% (95% CI 98-98.6%). Conclusions We successfully validated an ML model to detect circulatory shock in a prospective observational study. The model used only vital signs and showed moderate performance compared to the gold standard of clinician EMR review when applied to an ICU patient cohort.
Anticipatory thinking is necessary for managing risk in the safety-and missioncritical domains where AI systems are being deployed. We analyze the intersection of anticipatory thinking, the optimization paradigm, and metaforesight to advance our understanding of AI systems and their adaptive capabilities when encountering low-likelihood/high-impact risks. We describe this intersection as the anticipatory paradigm. We detail these challenges in concrete examples and propose new types of anticipatory thinking, towards a paradigm shift in how AI systems are evaluated.
Anticipatory thinking is a critical cognitive skill for successfully navigating complex, ambiguous systems in which individuals must analyze system states, anticipate outcomes, and forecast future events. For example, in military planning, intelligence analysis, business, medicine, and social services, individuals must use information to identify warnings, anticipate a spectrum of possible outcomes, and forecast likely futures in order to avoid tactical and strategic surprise. Existing methods for examining anticipatory thinking skill have relied upon task-specific behavioral measures or are resource-intensive, both of which are challenging to scale. Given the increasing importance of anticipatory thinking in many domains, developing a generic assessment of this skill and identifying the underlying cognitive mechanisms supporting it are paramount. The work reported here focuses on the development and validation of a general framework for ANticipatory Thinking Assessment (ANTA) that is rooted in widely used analytical methods as well as the divergent thinking literature. Two-hundred and ten participants completed the ANTA, which required them to anticipate possible risks, opportunities, trends or other uncertainties associated with a focal topic. Responses to the anticipatory thinking and divergent thinking tasks were rated by trained raters on a 5-point scale according to the uniqueness, specificity, and remoteness of responses. Results supported the ANTA’s construct validity, convergent validity, and discriminant validity. We also explored the relationship between ANTA scores and certain psychological traits and cognitive measures (need for cognition, need for closure, and mindfulness). Our findings suggest that the ANTA is a psychometrically valid instrument that may help researchers investigate anticipatory thinking in new contexts.
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