「uncertainty」の検索結果

Use when strengthening AAMAS reproducibility evidence for interaction claims, including proofs and game definitions, opponent and population sets, self-play protocols, random seeds, compute, uncertainty on strategic outcomes, baselines, and consistency between what the paper claims about agents and what the artifact can actually show.

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Reconstruct ancestral states at internal phylogenetic nodes for sequences (PAML codeml, IQ-TREE --ancestral, GRASP, FastML), discrete traits (corHMM hidden-rate Markov, ape::ace, phytools::make.simmap stochastic mapping, BayesTraits), and continuous traits (phytools::fastAnc, geiger Brownian/OU, RPANDA). Use when designing constructs for ancestral protein resurrection, tracing trait evolution along a tree, performing stochastic character mapping, testing models of trait evolution (BM vs OU vs EB), inferring ancestral genome content via Dollo or DTL reconciliation, or quantifying ancestral-state uncertainty for downstream comparative analyses.

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Builds QSAR / QSPR models using chemprop D-MPNN, MolFormer, Uni-Mol, ChemBERTa, random forest baselines, and Gaussian processes with explicit handling of OECD 5 principles, applicability domain (kNN, leverage, conformal prediction, Mahalanobis), scaffold-balanced splits, ensemble uncertainty, calibration (Platt, isotonic), feature importance (SHAP, atomic attribution), and prospective validation. Use when building target-specific predictive models from in-house bioassay data, ADMET endpoints, or selectivity profiles.

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Predicts ADMET properties using ADMETlab 3.0 (119 platform features, including 77 prediction models with modeled-endpoint uncertainty), ADMET-AI, DeepChem MolNet, and chemprop D-MPNN with explicit handling of OECD QSAR principles, applicability domain assessment, calibration, hERG/CYP/AMES endpoints, and PAINS / Lipinski / Ro5 / Veber / BBB druglikeness filters. Use when filtering compounds for drug-likeness, prioritizing leads by predicted safety, or building an in-house ADMET QSAR model.

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Analyzes differential transcript usage (DTU) and isoform switches with functional consequence prediction (NMD via 50nt rule, ORF disruption, protein domain loss/gain, signal peptide changes, IDR alterations, coding-potential shifts). Tools include IsoformSwitchAnalyzeR v2 (auto-selects satuRn for >5 reps else DEXSeq), the manual DRIMSeq -> DEXSeq/satuRn -> stageR DTU pipeline, and fishpond/swish for inferential-uncertainty-aware DTE. Distinguishes DTU from DGE and DTE; integrates external annotators (CPC2, Pfam, SignalP, IUPred2A or DeepTMHMM). Use when investigating how splicing differences alter protein function or trigger NMD-mediated degradation.

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Analyzes alternative splicing from PacBio Iso-Seq (HiFi, Kinnex/MAS-Iso-seq) and Oxford Nanopore (direct cDNA, direct RNA, R10.4.1+) long-read RNA-seq with full-isoform resolution. Tools include FLAIR (correct/collapse/quantify/diffSplice for PacBio + ONT), IsoQuant (de-novo or annotation-guided isoform discovery 2024 SOTA), Bambu (annotation-aware Bayesian discovery + quantification with Novel Discovery Rate), SQANTI3 (isoform classification: FSM/ISM/NIC/NNC + artifact flags), rMATS-long (event calling on long-read isoforms), and minimap2 (-ax splice:hq for HiFi; -ax splice -k14 for ONT cDNA; add -uf only for direct RNA or stranded cDNA preps). Solves microexon detection, recursive splicing, complex multi-exon isoforms, and DTU without transcript-quantification uncertainty. Use when short-read AS limitations (anchor length, complex isoforms, microexons, recursive splicing, transcript ambiguity) demand full-isoform resolution.

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Use this skill to classify tabular data end-to-end in MATLAB — load a dataset, prepare and clean it, select promising classifiers, train them, and compare accuracies with cross-validation, holdout, or hyperparameter optimization plus statistical tests. TRIGGER when: user asks to classify tabular data, pick classifiers for a dataset, compare classifier accuracy, run cross-validation or a holdout evaluation, or find the best model with statistical uncertainty. DO NOT TRIGGER when: user has non-tabular inputs (images, sequences, time series), wants a regression model, is training a specific neural network architecture (use matlab-train-network), or wants cost-sensitive learning or an arbitrary class-prior vector (this skill only supports the built-in uniform-prior toggle for imbalanced data).

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Apply systematic problem-solving techniques when stuck. Use for complexity spirals, innovation blocks, recurring patterns, assumption constraints, simplification cascades, scale uncertainty.

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Build or review source-backed descriptive, diagnostic, predictive, and prescriptive analysis for consequential decisions. Use when an agent must profile and safely prepare uploaded data, turn a real dataset or research question into a reproducible study, investigate drivers without overstating causality, validate a model, compare feasible actions under dependent uncertainty and tail risk, trace every parameter to evidence and approval, or produce an answer-first analytical report across health, business, finance, policy, engineering, operations, behavioral science, AI, or planning.

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Run a bounded customer proof of concept to test a consequential uncertainty. Use for a spike or pilot with a question and decision deadline, not a full rollout.

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Audits the transition from legal AI output to reliance, recommendation, execution, or real-world commitment. Use it before an AI-generated analysis, memo, contract review, compliance finding, or workflow output is acted upon to check whether authority, evidence, mandate, uncertainty, procedure, and review conditions remain sufficient.

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Audits legal AI outputs and workflows for honest compression: unnecessary complexity, false simplicity, excessive caveats, hidden uncertainty and poor cost per legally acceptable output.

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Use for due diligence, legal-financial risk review, investment or business transaction checklists, and preliminary screening where facts, documents, assumptions, legal uncertainty, debt/equity, assets/liabilities, contracts, tax, regulatory, compliance, technology/product, and financial-model issues must be separated clearly.

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Turn complex legal analysis into clear, commercially useful client-facing advice. Use this whenever the user has dense legal material — drafting, internal analysis, counsel notes, research memos, pleadings, a case update, or correspondence — and wants it converted into something a client can actually understand and act on. Trigger on phrases like 'explain this to the client', 'put this in plain English', 'translate this for a non-lawyer', 'turn this into client-facing advice', 'make this client-ready', 'draft a client update', or when the user shares legal analysis and asks 'what does this mean for them'. Also trigger when the user wants a board summary, litigation risk update, or call script derived from legal material. The skill preserves legal nuance, uncertainty, and risk rather than oversimplifying — it makes advice usable, not just simpler.

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Audits AI-assisted legal, compliance, governance, and institutional decisions before reliance to determine whether the responsible human or institution has enough access to the evidence, reasoning basis, uncertainty, authority, and review path to genuinely own the decision rather than merely approve, sign, or transmit it.

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Classes and statistical methods for large SNP association studies. This extends the earlier snpMatrix package, allowing for uncertainty in genotypes.

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Applies Eric Ries's Lean Startup methodology for building products under extreme uncertainty. Use when iterating toward product/market fit, designing MVPs, deciding whether to pivot or persevere, setting up actionable metrics, or accelerating the Build-Measure-Learn loop. Triggers include 'how do we test this idea fast', 'what should our MVP look like', 'our metrics look good but we're not growing', 'should we pivot', 'we're building features no one uses', 'how do we measure validated learning', 'vanity metrics vs real metrics', 'how to do innovation accounting'. NOT for companies with proven product/market fit scaling a known playbook (use Crossing the Chasm), not for determining Market Type (use Four Steps), not for sales methodology (use SPIN Selling), not for pricing strategy (use Monetizing Innovation).

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Advanced architecture stress analysis methodology for designing systems that survive unknown stresses. Load when --residuality flag is used or when designing high-uncertainty, mission-critical systems.

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Consensus cell type annotation: runs 10+ algorithms (KNN-Harmony/BBKNN/Scanorama/scVI, CellTypist, ONCLASS, Random Forest, SCANVI, SVM, XGBoost) on a labeled reference and transfers labels via majority voting. Outputs per-method labels, consensus, agreement score. Use when single-method annotation is insufficient or you need ensemble uncertainty for novel states.

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Deep generative models for single-cell omics: probabilistic batch correction (scVI), semi-supervised annotation (scANVI), CITE-seq RNA+protein (totalVI), transfer learning (scARCHES), and DE with uncertainty. Unified setup→train→extract API on AnnData. Use harmony-batch-correction for fast linear correction without deep learning; muon for multi-modal MuData workflows.

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Scores agent actions by expected gain, cost, uncertainty, and redundancy. Use when deciding whether to dispatch an agent or invoke a tool.

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Renamed to /model-assessment in v6 (removed in v7).

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Use when validating or evaluating a trained medical-imaging model. Audits split leakage and validation design, computes task-correct held-out metrics (Dice + HD95, AUROC + AUPRC, FROC, calibration), and covers uncertainty/OOD and Grad-CAM explainability, each with a gate.

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Use Chemprop 2.2.3 for molecular property prediction: CLI training, prediction, fingerprints, data validation, Python APIs, reaction/atom-bond tasks, uncertainty, hpopt, and conversion workflows.

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