Skill UI

PyMC is a powerful Python library for probabilistic programming and advanced Bayesian inference. This comprehensive guide details the full workflow for building, fitting, and validating complex Bayesian models. Learn to implement hierarchical structures, perform MCMC sampling (NUTS), conduct posterior predictive checks (PPC), and effectively quantify uncertainty using industry best practices.

PyMC is a powerful Python library designed for probabilistic programming and sophisticated Bayesian modeling. It enables users to build complex models, such as hierarchical structures and time series, and perform rigorous inference using methods like MCMC (NUTS) sampling and Variational Inference. Key features include model comparison (LOO, WAIC) and comprehensive diagnostic tools for uncertainty quantification.

This skill guides the creation and auditing of truthful, accessible, and publication-ready scientific figures. It emphasizes maintaining data integrity by separating universal scientific principles from journal-specific rules. Users learn proper encoding (e.g., using position on common scales, handling uncertainty/missing data) and implementing designs with scope-aware Python libraries like Matplotlib and Seaborn, ensuring compliance with WCAG standards and maximizing scientific rigor.

scvi-tools is a comprehensive Python framework utilizing deep generative models and variational inference for analyzing diverse single-cell data modalities. It excels in complex analyses such as probabilistic batch correction (scVI), multi-modal integration (MultiVI), and differential expression analysis with uncertainty. It supports single-cell RNA-seq, ATAC-seq, and various multi-omics datasets, providing advanced tools for modern genomic research.

A specialized tool designed to explore uncertain futures by mapping the entire possibility space. Instead of relying on a single prediction, the Oracle runs structured multi-branch scenario analyses (including Best, Worst, Wild Card, and Second-Order effects). It is ideal for stress-testing major decisions, performing contingency planning, and analyzing potential consequences when facing strategic forks or high-stakes uncertainty.

This skill converts complex, narrative technical documents, research excerpts, or natural language problem descriptions into a highly structured Mathematical Problem Specification (MPS). It systematically extracts variables, constraints, objectives, and uncertainty parameters. By adhering to a strict Zero-Inference Protocol, it ensures all extracted elements are strictly grounded in the source text, making it invaluable for formalizing real-world optimization, data science, and engineering problems.

A comprehensive guide outlining rigorous data analysis and reporting standards for geographic manuscripts. It covers spatial statistics, remote sensing accuracy, and qualitative interpretation, emphasizing spatial honesty, quantifying uncertainty, and ensuring results are robust across different scales and units.

A comprehensive set of guidelines for generating maps, figures, and tables for academic journals. This guide emphasizes cartographic standards, statistical rigor, and maximizing the visual argument, ensuring that all exhibits are reproducible, legible in print, and adhere to strict word count limitations. It covers everything from projection choice and data normalization to model plot interpretation and handling spatial uncertainty.

This skill guides researchers on the mandatory, rigorous evaluation of complex systems models (e.g., AgSy). It details best practices for model validation, emphasizing the comparison of observed vs. simulated data using independent, held-out datasets. Key components covered include standard fit statistics (RMSE, NSE), sensitivity analysis (identifying core drivers), uncertainty propagation, and multi-objective trade-off/scenario analysis to ensure scientific credibility.

This guide provides rigorous guidelines for creating high-quality figures and tables for complex systems manuscripts, especially in agricultural science. It emphasizes shifting focus from single-factor bar charts to systemic visualizations that reveal interactions, trade-offs (e.g., Pareto fronts), model dynamics, resource flows (Sankey diagrams), and model performance (observed-vs-simulated fit). Exhibits must be self-contained, reproducible, and convey uncertainty.

This skill guides researchers on how to transform complex agricultural systems model results into actionable, honest, and scoped implications for decision-makers. It teaches authors to move beyond merely restating results by identifying the specific actors, articulating the necessary trade-offs, and clearly defining the system boundaries and uncertainty limits, ensuring the paper informs a decision rather than just demonstrating methods.

This guide provides strict guidelines for designing, auditing, and reporting empirical or simulation experiments, particularly for theoretical machine learning and statistics papers. It emphasizes mapping every empirical claim to specific evidence, ensuring statistical rigor (e.g., reporting uncertainty, baselines, seeds), and validating theoretical assumptions rather than optimizing for leaderboards. Essential for research reproducibility.