A prediction-focused approach to personality modeling.
Ontology highlight
ABSTRACT:
SUBMITTER: Lavi G
PROVIDER: S-EPMC9314364 | biostudies-literature |
REPOSITORIES: biostudies-literature
Similar Datasets
Project description:Mapping of orthologous genes among species serves an important role in functional genomics by allowing researchers to develop hypotheses about gene function in one species based on what is known about the functions of orthologs in other species. Several tools for predicting orthologous gene relationships are available. However, these tools can give different results and identification of predicted orthologs is not always straightforward.We report a simple but effective tool, the Drosophila RNAi Screening Center Integrative Ortholog Prediction Tool (DIOPT; http://www.flyrnai.org/diopt), for rapid identification of orthologs. DIOPT integrates existing approaches, facilitating rapid identification of orthologs among human, mouse, zebrafish, C. elegans, Drosophila, and S. cerevisiae. As compared to individual tools, DIOPT shows increased sensitivity with only a modest decrease in specificity. Moreover, the flexibility built into the DIOPT graphical user interface allows researchers with different goals to appropriately 'cast a wide net' or limit results to highest confidence predictions. DIOPT also displays protein and domain alignments, including percent amino acid identity, for predicted ortholog pairs. This helps users identify the most appropriate matches among multiple possible orthologs. To facilitate using model organisms for functional analysis of human disease-associated genes, we used DIOPT to predict high-confidence orthologs of disease genes in Online Mendelian Inheritance in Man (OMIM) and genes in genome-wide association study (GWAS) data sets. The results are accessible through the DIOPT diseases and traits query tool (DIOPT-DIST; http://www.flyrnai.org/diopt-dist).DIOPT and DIOPT-DIST are useful resources for researchers working with model organisms, especially those who are interested in exploiting model organisms such as Drosophila to study the functions of human disease genes.
| S-EPMC3179972 | biostudies-literature
Project description:Deep machine learning is expanding the conceptual framework and capacity of computational compound design, enabling new applications through generative modeling. We have explored the systematic design of covalent protein kinase inhibitors by learning from kinome-relevant chemical space, followed by focusing on an exemplary kinase of interest. Covalent inhibitors experience a renaissance in drug discovery, especially for targeting protein kinases. However, computational design of this class of inhibitors has thus far only been little investigated. To this end, we have devised a computational approach combining fragment-based design and deep generative modeling augmented by three-dimensional pharmacophore screening. This approach is thought to be particularly relevant for medicinal chemistry applications because it combines knowledge-based elements with deep learning and is chemically intuitive. As an exemplary application, we report for Bruton's tyrosine kinase (BTK), a major drug target for the treatment of inflammatory diseases and leukemia, the generation of novel candidate inhibitors with a specific chemically reactive group for covalent modification, requiring only little target-specific compound information to guide the design efforts. Newly generated compounds include known inhibitors and characteristic substructures and many novel candidates, thus lending credence to the computational approach, which is readily applicable to other targets.
| S-EPMC8778003 | biostudies-literature
Project description:Animal personalities are an important factor that affects the dispersal of animals. In the context of aquatic species, dispersal modeling needs to consider that most freshwater ecosystems are highly fragmented by barriers reducing longitudinal connectivity. Previous research has incorporated such barriers into dispersal models under the neutral assumption that all migrating animals attempt to ascend at all times. Modeling dispersal of animals that do not perform trophic or reproductive migrations will be more realistic if it includes assumptions of which individuals attempt to overcome a barrier. We aimed to introduce personality into predictive modeling of whether a nonmigratory invasive freshwater fish (the round goby, Neogobius melanostomus) will disperse across an in-stream barrier. To that end, we experimentally assayed the personalities of 259 individuals from invasion fronts and established round goby populations. Based on the population differences in boldness, asociability, and activity, we defined a priori thresholds with bolder, more asocial, and more active individuals having a higher likelihood of ascent. We then combined the personality thresholds with swimming speed data from the literature and in situ measurements of flow velocities in the barrier. The resulting binary logistic regression model revealed probabilities of crossing a barrier which depended not only on water flow and fish swimming speed but also on animal personalities. We conclude that risk assessment through predictive dispersal modeling across fragmented landscapes can be advanced by including personality traits as parameters. The inclusion of behavior into modeling the spread of invasive species can help to improve the accuracy of risk assessments.
| S-EPMC5243775 | biostudies-literature
Project description:Conventional item response theory (IRT) modeling of personality responses considers two item characteristics-location and discrimination-but only one person characteristic-location or trait level. An IRT modeling approach that jointly considers item and person discriminations, however, is thought to be more realistic and appropriate in this domain and has several potential advantages. This article develops a model of this type for unidimensional binary responses together with procedures for estimating item and person parameters and assessing model appropriateness (including person fit). A series of preliminary simulations suggests that the approach is feasible, and a real-data example illustrates the potential advantages with respect to the standard two-parameter model. Limitations of the proposal and further work are also discussed.
| S-EPMC5978483 | biostudies-literature
Project description:Binding affinity prediction is frequently addressed using computational models constructed solely with molecular structure and activity data. We present a hybrid structure-guided strategy that combines molecular similarity, docking, and multiple-instance learning such that information from protein structures can be used to inform models of structure-activity relationships. The Surflex-QMOD approach has been shown to produce accurate predictions of binding affinity by constructing an interpretable physical model of a binding site with no experimental binding site structural information. We introduce a method to integrate protein structure information into the model induction process in order to construct more robust physical models. The structure-guided models accurately predict binding affinities over a broad range of compounds while producing more accurate representations of the protein pockets and ligand binding modes. Structure-guidance for the QMOD method yielded significant performance improvements, both for affinity and pose prediction, especially in cases where predictions were made on ligands very different from those used for model induction.
| S-EPMC3851759 | biostudies-literature
Project description:There is a wide, and continuously widening, gap between the number of proteins known only by their amino acid sequence versus those structurally characterized by direct experiment. To close this gap, we mostly rely on homology-based inference and modeling to reason about the structures of the uncharacterized proteins by using structures of homologous proteins as templates. With the rapidly growing size of the Protein Data Bank, there are often multiple choices of templates, including multiple sets of coordinates from the same protein. The substantial conformational differences observed between different experimental structures of the same protein often reflect function related structural flexibility. Thus, depending on the questions being asked, using distant homologs, or coordinate sets with lower resolution but solved in the appropriate functional form, as templates may be more informative. The ModFlex server (https://modflex.org/) addresses this seldom mentioned gap in the standard homology modeling approach by providing the user with an interface with multiple options and tools to select the most relevant template and explore the range of structural diversity in the available templates. ModFlex is closely integrated with a range of other programs and servers developed in our group for the analysis and visualization of protein structural flexibility and divergence.
| S-EPMC8428579 | biostudies-literature
Project description:Clarifying individual differences that predict resilience or vulnerability to emotional distress is crucial for identifying etiological factors contributing to affective disturbances, and to promoting emotional well-being. Despite recent progress identifying specific brain regions and personality traits, it remains unclear whether there are common factors underlying the structural aspects of the brain and the personality traits that, in turn, protect against symptoms of emotional distress. In the present study, an integrative structural equation model was developed to examine the associations among (1) a latent construct of Control, representing the volumes of a system of prefrontal cortical (PFC) regions including middle, inferior, and orbital frontal cortices; (2) a latent construct of Resilience personality traits including cognitive reappraisal, positive affectivity, and optimism; and (3) Anxiety and Depression symptoms, in a sample of 85 healthy young adults. Results showed that the latent construct of PFC volumes positively predicted the latent construct of Resilience, which in turn negatively predicted Anxiety. Mediation analysis confirmed that greater latent PFC volume is indirectly associated with lower Anxiety symptoms through greater latent trait Resilience. The model did not show a significant mediation for Depression. These results support the idea that there are common volumetric and personality factors that help protect against symptoms of emotional distress. These findings provide strong evidence that such brain-personality-symptom approaches can provide novel insights with valuable implications for understanding the interaction of these factors in healthy and clinically diagnosed individuals.
| S-EPMC7219678 | biostudies-literature
Project description:Prediction of motor diagnosis in Huntington's disease (HD) can be improved by incorporating other phenotypic and biological clinical measures in addition to cytosine-adenine-guanine (CAG) repeat length and age.The objective was to compare various clinical and biomarker trajectories for tracking HD progression and predicting motor conversion.Participants were from the PREDICT-HD study. We constructed a mixed-effect model to describe the change of measures while jointly modeling the process with time to HD diagnosis. The model was then used for subject-specific prediction. We employed the time-dependent receiver operating characteristic (ROC) method to assess the discriminating capability of the measures to identify high and low risk patients. The strongest predictor was used to illustrate the dynamic prediction of the disease risk and future trajectories of biomarkers for three hypothetical patients.1078 individuals were included in this analysis. Five longitudinal clinical and imaging measures were compared. The putamen volume had the best discrimination performance with area under the curve (AUC) ranging from 0.74 to 0.82 over time. The total motor score showed a comparable discriminative ability with AUC ranging from 0.69 to 0.78 over time. The model showed that decreasing putamen volume was a significant predictor of motor conversion. A web-based calculator was developed for implementing the methods.By jointly modeling longitudinal data with time-to-event outcomes, it is possible to construct an individualized dynamic event prediction model that renews over time with accumulating evidence. If validated, this could be a valuable tool to guide the clinician in predicting age of onset and potentially rate of progression.
| S-EPMC5505650 | biostudies-literature
Project description:AimsThe heterogeneity in Gestational Diabetes Mellitus (GDM) risk factors among different populations impose challenges in developing a generic prediction model. This study evaluates the predictive ability of existing UK NICE guidelines for assessing GDM risk in Singaporean women, and used machine learning to develop a non-invasive predictive model.MethodsData from 909 pregnancies in Singapore's most deeply phenotyped mother-offspring cohort study, Growing Up in Singapore Towards healthy Outcomes (GUSTO), was used for predictive modeling. We used a CatBoost gradient boosting algorithm, and the Shapley feature attribution framework for model building and interpretation of GDM risk attributes.ResultsUK NICE guidelines showed poor predictability in Singaporean women [AUC:0.60 (95% CI 0.51, 0.70)]. The non-invasive predictive model comprising of 4 non-invasive factors: mean arterial blood pressure in first trimester, age, ethnicity and previous history of GDM, greatly outperformed [AUC:0.82 (95% CI 0.71, 0.93)] the UK NICE guidelines.ConclusionsThe UK NICE guidelines may be insufficient to assess GDM risk in Asian women. Our non-invasive predictive model outperforms the current state-of-the-art machine learning models to predict GDM, is easily accessible and can be an effective approach to minimize the economic burden of universal testing & GDM associated healthcare in Asian populations.
| S-EPMC7612635 | biostudies-literature
Project description:Introduction Openness, conscientiousness, extroversion, agreeableness and neuroticism are known as the Big Five personality traits (BFPT). They are theoretical building blocks of the personality and comprise wide and interconnected spectra. Artificial intelligence (AI) could help to grasp their complexity. Objectives To investigate whether AI could predict the BFPT from themselves. Methods Data from 2,697 questionnaires were analysed using an AI. The short form of the International Personality Item Pool was used to assess the BFPT. Four of the BFPT scores were employed to predict the fifth one and the procedure was repeated for all of them alternatively. The AI was conservatively tuned to maximize the one-way random intraclass correlation coefficient (ICC) between predicted and real values. Their Pearson’s r was calculated too. The free and open source programming language R was used for all the analyses. Dataset source: Hansson, Isabelle; Berg, Anne Ingeborg; Thorvaldsson, Valgeir (2018), “Can personality predict longitudinal study attrition? Evidence from a population-based sample of older adults”, Mendeley Data, V1, doi: 10.17632/g3jx8zt2t9.1 Results Openness, conscientiousness, extroversion, agreeableness and neuroticism predictions obtained ICC of 0.219, 0.146, 0.306, 0.354, 0.121 and Pearson’s r of 0.254, 0.149, 0.393, 0.446, 0.122 respectively. The results for extroversion and agreeableness were indicative of fair performance. Conclusions AI might be useful to predict personality traits, mainly extroversion and agreeableness. This could be utile in many situations, such as dealing with missing data or deciding whether to formally test someone. Finally, the AI used in this study is freely available, allowing anyone to experiment.
| S-EPMC9475767 | biostudies-literature