「bias」の検索結果

Normalizes and transforms RNA-seq count matrices for DE, visualization, clustering, and ML. Covers between-sample (TMM, TMMwsp, RLE/median-of-ratios, upper quartile), within-sample (TPM, FPKM/RPKM), variance-stabilizing (VST, rlog, log-CPM), GC-content correction (cqn, EDASeq), and single-cell (scran deconvolution, scanpy normalize_total). Encodes the composition-bias rationale, the "most genes not DE" assumption and its catastrophic failure modes (MYC amplification, apoptosis, viral host shutoff, prokaryotic stress), the "lengthScaledTPM is not TPM" naming trap, the "TPM is not for DE" rule, the blind=TRUE vs FALSE decision, ERCC spike-in normalization (SBN), and the single-cell zero-inflation breakdown of TMM/RLE. Use when choosing or applying normalization, debugging shifted-MA-plot diagnostics, handling zero-heavy single-cell data, or correcting GC bias.

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Normalize read-depth copy-ratio profiles and segment them into copy-number regions using circular binary segmentation (CBS, DNAcopy), hidden Markov models, HaarSeg, and fused-lasso methods. Covers GC-content, mappability, and replication-timing (wave-artifact) bias correction, panel-of-normals/PCA denoising, diploid-baseline centering, and algorithm selection by sequencing depth and event size. Use when choosing a segmentation algorithm, correcting depth bias, diagnosing oversegmentation or a mis-centered baseline, tuning CBS or HMM parameters, or understanding why a downstream CNV caller produced fragmented or shifted segments.

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Detects allele-specific transcription factor or histone modification binding from heterozygous-variant ChIP-seq using WASP (reference-bias filter; mandatory upstream), RASQUAL (joint QTL + bias-corrected testing), BaalChIP (Bayesian beta-binomial with copy-number-aware overdispersion), and AlleleSeq (personalized diploid genome). Handles imprinted-locus awareness, X-inactivation artifacts, cancer copy-number imbalance, and integration with downstream caQTL / bQTL mapping. Use when identifying variants with allelic effects on TF binding, fine-mapping causal regulatory variants, validating deep-learning variant predictions, or characterizing cis-acting regulatory effects.

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Identifies differentially bound ChIP-seq regions between conditions using DiffBind, csaw (sliding windows), DESeq2/edgeR/PyDESeq2 on count matrices, NormR (control-aware), or MAnorm2. Distinguishes three distinct normalization problems (composition bias, trended bias, global shifts) and matches each to its appropriate fix including spike-in scaling. Use when comparing ChIP-seq binding between experimental conditions, choosing normalization for global vs local changes, integrating spike-in data, or reconciling DiffBind/DESeq2 disagreement.

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Detect transcription factor binding footprints in ATAC-seq using TOBIAS, HINT-ATAC, Wellington, or scprinter. Use when identifying bound TF sites within accessible regions, correcting Tn5 insertion bias before footprinting, choosing between cleavage-based and aggregate-based footprinters, or comparing differential TF activity between conditions.

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Estimates bivariate genetic correlation (rg) between traits from GWAS summary statistics or individual-level genotypes using cross-trait LDSC, HDL, LAVA, rho-HESS, GREML-bivariate, Popcorn, and HDL-L. Use when quantifying shared genetic architecture between two traits, screening MR validity before causal inference, distinguishing global from locus-level rg, estimating trans-ancestry rg, separating partial from full causation via LCV gcp, or producing a STROBE-MR-compliant cross-trait sensitivity battery. Cross-trait LDSC intercept absorbs sample overlap and is NOT a bias; HDL is biased under sample overlap above ~5%. High rg between exposure and outcome motivates CHP-aware MR sensitivity (CAUSE, LHC-MR).

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Use when the user has a judge/grader and human-labeled data, and wants to measure how well the judge agrees with humans, detect systematic biases, determine whether automatic evaluation can replace human review, or build a human-reduction roadmap. Also use when the user mentions calibration, TPR/TNR, judge validation, inter-rater agreement, Cohen's kappa, bias detection, or "is my automatic evaluation trustworthy." Merges the calibrate and align functions into one skill.

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Check an educational practice or task for cultural bias, WEIRD assumptions, and cross-cultural validity. Use when adapting resources for diverse contexts or questioning universal claims.

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Use when `evidence-review` has an extraction table and needs lightweight risk-of-bias fields.

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Apply the NIST AI Risk Management Framework (AI RMF 1.0) and adjacent guidance to AI / ML systems — model lifecycle governance, fairness and bias evaluation, robustness, transparency, accountability, third-party model risk, monitoring for drift, and AI incident response. Broader than prompt-injection (which is the security slice). Use when the user mentions 'AI risk,' 'AI governance,' 'NIST AI RMF,' 'AI compliance,' 'ML governance,' 'model risk management,' 'AI fairness,' 'AI bias,' 'algorithmic accountability,' 'AI Bill of Rights,' 'EU AI Act,' 'AI transparency,' 'model card,' 'AI red team,' 'AI safety,' 'responsible AI,' 'model drift,' 'concept drift,' 'AI monitoring,' 'AI incident,' or needs to assess or govern an AI / ML system.

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Use when the user wants to analyze dataset bias, create stratified samples, evaluate fairness, or plan dataset collection. Triggers on phrases like "dataset bias", "stratified sample", "class imbalance", "data distribution", "fairness analysis", or "ethical review".

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Inverts burden of proof for code additions. Use when reviewing PRs, planning refactors, or running unbloat to challenge every addition's necessity.

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Audits changes for additive bias and Iron Law compliance. Use when reviewing completed work before merging or after AI-assisted implementation.

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Use when auditing a manuscript item by item against a reporting guideline or risk-of-bias tool. Covers 49 reporting guidelines and risk-of-bias tools (STROBE, CONSORT, STARD, TRIPOD+AI, PRISMA, QUADAS and more), marking each item PRESENT, PARTIAL or MISSING. Not a reviewer critique (/self-review).

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This skill should be used when the user asks to "implement LLM-as-judge", "compare model outputs", "create evaluation rubrics", "mitigate evaluation bias", or mentions direct scoring, pairwise comparison, position bias, evaluation pipelines, or automated quality assessment.

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Addresses healthcare AI privacy at the intersection of HIPAA and the EU AI Act for clinical decision support systems. Covers training data PHI handling, model transparency and explainability, patient rights in algorithmic decisions, FDA/OCR regulatory coordination, and bias monitoring. Keywords: healthcare AI, HIPAA, AI Act, clinical decision support, PHI training data, model transparency.

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QA an analysis before sharing with stakeholders — methodology checks, accuracy verification, and bias detection. Use when reviewing an analysis for errors, checking for survivorship bias, validating aggregation logic, or preparing documentation for reproducibility.

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Think and work like an expert Gerontologist. Use when a task calls for Gerontologist judgment. Reasons from senescence hallmarks, frailty, multi-morbidity, and life-course exposures through validated instruments (Fried phenotype, Rockwood CFS, SPPB/gait speed), epigenetic clocks (Horvath, PhenoAge, GrimAge), competing-risk survival (Fine-Gray), and NIA cohorts (HRS, NHATS, ITP) while treating survivor bias, differential attrition, healthy-volunteer bias, and frail-subset toxicity as first-class failure modes.

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Think and work like an expert Hydrologist. Use when a task calls for Hydrologist judgment. Reasons from hydrologic-cycle closure (P = ET + Q + ΔS + I), runoff-generation mechanisms, and channel routing through HEC-HMS, HEC-RAS, the National Water Model, and split-sample KGE/NSE/PBIAS calibration, while treating post-flood rating-curve shifts, radar QPE bias, snow/rain misclassification, and non-stationarity in extremes as first-class failure modes.

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Think and work like an expert Emergency Medicine Researcher. Use when a task calls for Emergency Medicine Researcher judgment. ED trial design expert for pragmatic and cluster RCTs, time-zero and immortal-time bias in acute cohorts, NIHSS/SOFA/qSOFA and ESI/CTAS triage, NEDS/NHAMCS registries, and CONSORT/SPIRIT reporting with Hawthorne and selection-bias failure modes.

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Think and work like an expert Computer Graphics Researcher. Use when a task calls for Computer Graphics Researcher judgment. Reasons from the rendering equation, Monte Carlo bias/variance, sampling theory, and BSDF energy conservation through pbrt-v4/Mitsuba 3 references, MIS/ReSTIR/path guiding, DXR 1.2 real-time stacks, 3DGS and NerfBaselines protocols, FLIP/ColorVideoVDP evaluation, OpenUSD/MaterialX/OpenPBR interchange, and ACES 2/OCIO color while treating unconverged references, unequal-time comparisons, denoiser and temporal-reuse bias, scene- vs display-referred color errors, and white-furnace energy failures as first-class failure modes.

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Think and work like an expert Astrostatistician. Use when a task calls for Astrostatistician judgment. Reasons from selection functions, censored flux limits, and look-elsewhere trial factors through Cobaya/emcee/dynesty cosmology, GP-coupled exoplanet inference, Landy–Szalay clustering, photo-z σNMAD calibration, and SBI (sbi/LtU-ILI) while treating Malmquist bias, prior-driven tensions, and detrend-then-fit transit bias as first-class failure modes.

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Detect transcription factor binding footprints in ATAC-seq using TOBIAS, HINT-ATAC, Wellington, or scprinter. Use when identifying bound TF sites within accessible regions, correcting Tn5 insertion bias before footprinting, choosing between cleavage-based and aggregate-based footprinters, or comparing differential TF activity between conditions.

日本語の概要は準備中です。原文の説明を表示しています。

Identifies differentially bound ChIP-seq regions between conditions using DiffBind, csaw (sliding windows), DESeq2/edgeR/PyDESeq2 on count matrices, NormR (control-aware), or MAnorm2. Distinguishes three distinct normalization problems (composition bias, trended bias, global shifts) and matches each to its appropriate fix including spike-in scaling. Use when comparing ChIP-seq binding between experimental conditions, choosing normalization for global vs local changes, integrating spike-in data, or reconciling DiffBind/DESeq2 disagreement.

日本語の概要は準備中です。原文の説明を表示しています。