「reproducibility」の検索結果

Designs genomics experiments so technical nuisance variation (batch, lane, plate, flow cell, operator, reagent lot, processing day) is balanced against the biological variable of interest and therefore estimable rather than confounded, using constrained sample-to-batch assignment (designit, OSAT), the confounder/mediator/collider distinction, and the principle that no post-hoc correction recovers a fully confounded design. Covers detecting hidden batches with surrogate variable analysis, a decision table for downstream correction (ComBat-seq, RUVSeq, SVA) whose execution is deferred to differential-expression/batch-correction, and reproducibility metadata. Use when assigning samples to sequencing batches/lanes/plates, avoiding batch-condition confounding, deciding whether a design is salvageable by correction, choosing a correction method, or estimating the number of hidden batches. For the experimental unit, randomization, and blocking concepts see experimental-design/randomization-blocking.

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Performs differential expression on bulk RNA-seq count data with edgeR's negative-binomial GLM and quasi-likelihood F-test framework. Covers DGEList construction, filterByExpr, TMM/TMMwsp normalization, robust dispersion estimation, glmQLFit/glmQLFTest, TREAT for magnitude-bounded hypotheses, contrasts via no-intercept designs, voom and voomWithQualityWeights for heterogeneous samples, and the edgeR v4 bias-corrected APL changes. Use when running bulk DE with edgeR, choosing edgeR over DESeq2 (small n, transcript DE via catchSalmon, large samples), needing TREAT for a fold-change-threshold hypothesis, troubleshooting v3-to-v4 reproducibility, building paired or interaction designs, or handling library-quality heterogeneity.

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Queries myvariant.info BioThings aggregator for ClinVar, gnomAD, dbSNP, dbNSFP, COSMIC, CADD, and CIViC annotations in batched, version-tracked requests. Use when annotating variant lists from multiple databases simultaneously without managing per-source APIs, and when reproducibility-grade analyses require recording source data versions via _meta.

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Comprehensive quality control for CLIP-seq libraries (eCLIP, iCLIP, iCLIP2, PAR-CLIP) covering library complexity (preseq), FRiP, IDR replicate reproducibility, read-distribution metagene, SMInput vs IgG control rationale, rRNA / snoRNA contamination, fragment-length distribution, and ENCODE-compliance thresholds. Use when assessing whether a CLIP library passed, deciding lenient vs stringent peak thresholds, comparing replicates with IDR rescue and self-consistency ratios, or distinguishing failed IP from over-amplified library.

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Review and revise academic papers with a senior-reviewer workflow. Use when an AI research/coding agent needs to work on an existing paper draft, PDF, LaTeX project, Word document, markdown manuscript, rejected paper, or paper idea that already has a concrete direction, and produce: paper maps, weakness audits, insight/novelty checks, reviewer objections, claim-experiment matrices, theory/proof checks, experiment plans, statistics/reproducibility audits, figure/table audits, ethics/compliance checks, revision plans, detailed section edits, or final submission checklists.

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Structured, reproducible analysis documentation. Use when documenting analysis findings, creating analysis notebooks, ensuring reproducibility, or building analysis archives for future reference.

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Use when you need framework-agnostic Docker and container image guidance for Java projects - Dockerfile design, multi-stage Maven builds, jlink custom runtimes, micro runtime distributions such as Alpaquita, JVM container ergonomics, non-root execution, image metadata, .dockerignore, reproducible builds, vulnerability scanning, SBOM awareness, and production-safe container defaults. This should trigger for requests such as Review Java Dockerfile; Improve Docker image security; Add jlink runtime to a Java container; Add containerization to a Java project; Optimize Java container image size; Review Docker build reproducibility. Part of Plinth Toolkit

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Check a mathematical-modeling paper's in-text citations, bibliography, appendix length and content, code, supporting files, reproducibility, consistency, and anonymity. Use when the user provides a paper or related materials and wants one consolidated P0-P3 audit; do not generate or invent missing sources or programs.

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Use when the user wants to prepare code for open-source release, create reproducible research artifacts, or structure a repository for publication. Triggers on phrases like "publish code", "open source release", "reproducibility", "research repository", "code release", or "prepare for publication".

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Evaluating scientific evidence and claims. Covers study design hierarchy (RCT to expert opinion), effect sizes (OR, RR, NNT, Cohen's d), confounding, p-value vs clinical significance, GRADE quality assessment, reproducibility, and bias types (selection, information, confounding, reporting). Use when reading a paper or assessing claims.

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Structured peer review of manuscripts and grants. 7-stage evaluation: initial assessment, section review, statistical rigor, reproducibility, figure integrity, ethics, writing. Covers CONSORT/STROBE/PRISMA and report structure. For evidence quality see scientific-critical-thinking; scoring see scholar-evaluation.

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Use when an analysis is complete and verified, and you need to decide how to report it and archive the work for reproducibility

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Use when reviewing mathematical validity, evidence, reproducibility, figures or a submission draft.

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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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Break down full ARR (ACL Rolling Review) reviewer responses into structured rebuttal units. Use when input contains ARR reviewer fields (Paper Summary, Strengths, Weaknesses, Comments/Suggestions) and numeric scores (Confidence, Soundness, Excitement, Overall Assessment, Reproducibility). Splits weaknesses and comments/suggestions into granular response items while preserving original wording for quoted issues.

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Think and work like an expert Machine Learning Researcher. Use when a task calls for Machine Learning Researcher judgment. Reasons from population risk, double descent, and inductive bias; enforces sacred test sets, hierarchical ablations, nested CV, and HELM/Dynabench-aware benchmarking; reports with NeurIPS and Pineau reproducibility checklists while treating leakage, meta-overfitting, benchmark contamination, Goodhart gaming, and seed variance as first-class failure modes.

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Think and work like an expert Experimental Physicist. Use when a task calls for Experimental Physicist judgment. Reasons from GUM error budgets, traceable calibration chains, and multiplied signal-chain transfer functions — separating Type A and Type B uncertainty, null runs, and ELN-linked reproducibility before precision or discovery claims.

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Think and work like an expert Computational Linguist. Use when a task calls for Computational Linguist judgment. Reasons from UD/PTB formalisms, validate.py/eval.py (LAS/MLAS/ELAS), and evalb .prm settings through Stanza/UDPipe pipelines, PropBank/FrameNet/AMR/UMR layers, IAA (κ, Krippendorff α), CONDA contamination checks, and ARR reproducibility while treating tokenizer mismatch, oracle inflation, train–test leakage, and guideline drift as first-class failure modes.

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Think and work like an expert Deep Learning Scientist. Use when a task calls for Deep Learning Scientist judgment. Reasons from CNN/Transformer inductive bias, Li et al. loss landscapes, grokking/mode connectivity, and Kaplan/Chinchilla scaling (~20 tokens/param); designs ResNet/ViT/DiT/MoE/FlashAttention stacks with FLOPs-matched ablations; trains AdamW+cosine/WSD via Megatron-FSDP/DeepSpeed; evaluates FID/MMLU-Pro/MMLU-CF with lm-eval decontamination and Pineau/NeurIPS reproducibility checklists.

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Think and work like an expert AI Researcher. Use when a task calls for AI Researcher judgment. Reasons from data generating processes, inductive biases, and compute-data-algorithm trade-offs through train/val/test discipline, seed sweeps, ablation ladders, and standards like NeurIPS reproducibility checklists, model cards, and lm-eval-harness, while treating data leakage (Kapoor & Narayanan taxonomy), benchmark contamination, spurious correlations, and reward-model overoptimization as first-class failure modes.

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Think and work like an expert Bioinformatician. Use when a task calls for Bioinformatician judgment. Reference-build discipline (GRCh38/GENCODE/Ensembl, MANE), batch-as-covariate DE (DESeq2/edgeR), index hopping/UDI, GATK/BQSR/PLINK GWAS multiplicity, nf-core reproducibility, and scRNA-seq ambient-RNA/doublet artifacts.

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Build and operate rights-aware Bria FIBO and FIBO Lite image-generation workflows with structured prompts, reference images, asynchronous status handling, webhooks, cost gates, and safe artifact downloads. Use when a user asks for Bria/FIBO generation, refinement, inspiration, reproducibility, hosted API integration, or a licensed-data image workflow; do not use for FIBO Edit, video, generic image editing, or third-party FIBO gateways.

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Provider-independent production workflow for agents assembling, auditing, executing, and handing off ComfyUI node-graph workflows for image, video, upscale, inpaint, conditioning, and batch media generation; use when a task involves ComfyUI workflow JSON/API graphs, model and custom-node inventories, reproducibility, provenance, safety/rights review, local or cloud execution hygiene, or production QA.

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Plan, prompt, execute, troubleshoot, and quality-control Black Forest Labs FLUX image generation and editing across the BFL direct API and licensed local/open-weight deployments. Use for FLUX.2 model selection, text-to-image, single- or multi-reference editing, typography, exact-color work, mask-based erase/inpainting, outpainting, API integration, reproducibility, deployment licensing, and production rights or safety decisions; also use when migrating or maintaining legacy FLUX.1/FLUX1.1 workflows.

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