Results for “matrix”

Drafts a standalone API Acceptable Use Policy (AUP) for incorporation by reference into a master API license or terms-of-service agreement. Produces a publication-ready template with prohibited-use matrix, developer security checklist, graduated enforcement framework, AI/ML training restrictions, and versioning playbook. Trigger when a user needs to draft or update an API AUP, separate behavioral rules from core API terms, define prohibited API uses, add enforcement or change-management mechanics, or mentions acceptable use policy, developer security requirements, or API enforcement.

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Manage 4todo (4to.do) from chat. Capture tasks, prioritize with the Eisenhower Matrix, reorder, complete, and manage recurring tasks across workspaces.

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planning promotion terminal-state negative matrix

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DiT 计算模块（L3）：把**已定位的 DiT 计算瓶颈**落成特性级选档与实施—— 量化档（W8A16 / W4A16 / W8A8 系列 / W4A4 / MXFP8 / FA 量化）、稀疏（rf_v2 / ada_bsa）、 缓存（DiTCache / AttentionCache / 时间步优化）、编译启用（MindieSDBackend / Pattern 融合 / ACLGraph） 的**开不开、开哪一档、怎么开、怎么复验**；依据是 `docs/zh/features/*`（特性真源）+ framework-integration/references/framework-support-matrix.md（支持状态）。 即使用户只说"这个模型怎么加速""量化/稀疏/Cache 怎么选怎么开""要不要开量化、开哪一档""这个档位开了有没有效果" 而未提 profiling，也应触发。 **入口条件**：瓶颈点已明确（用户带一句实测锚点，或编排层交付标签）时由域入口 `performance-optimization` 按标签分发到本技能；**瓶颈未明（"怎么加速 / 跑通 / 采 profile"）先走 `model-auto-optimization` 定位**，不在本技能内做占比分析。 near-miss：多卡并行形态 / 通信掩盖 / TP·offload 选型 → `dit-parallel-opt`；VAE 解码段与 host 固定开销 → 各自模块（VAE / host）；单算子实现级实测选型（mindie_bench）→ `benchmark-dev`； 需要新增 pattern / 算子才能落地本档 → `pattern-dev` / `operator-dev`；框架侧开关与使能验证 → `framework-integration`；量化器位级契约与精度对齐（编码公式 / 舍入 / scale 粒度）→ `quantization-dev`；精度验收判据 → `accuracy-gate`；数字入库口径 → `perf-gate`。

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Build production CI/CD pipelines with GitHub Actions. Implements matrix builds, caching, deployments, testing, security scanning. Use for automated testing, deployments, release workflows. Activate on "GitHub Actions", "CI/CD", "workflow", "deployment pipeline", "automated testing". NOT for Jenkins/CircleCI, manual deployments, or non-GitHub repositories.

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Validates permission inheritance between parent and child agents. Ensures child permissions are equal to or more restrictive than parent. Activate on 'validate permissions', 'permission check', 'inheritance validation', 'permission matrix', 'security validation'. NOT for runtime enforcement (use dag-scope-enforcer) or isolation management (use dag-isolation-manager).

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Implement Google's Material Design 3 (Material You) UI system. Primary: Jetpack Compose Material3 (MaterialTheme, components, adaptive layout). Also Flutter and limited web (@material/web, maintenance mode). Covers tokens, 30+ components, layout, theming, M3 Expressive (platform matrix), and accessibility. Use when: "material design", "MD3", "material you", "Jetpack Compose", "MaterialTheme", "material component", "md3 button".

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Infer gene regulatory networks from bulk or general expression data with mutual-information (ARACNe) and tree-ensemble (GENIE3, GRNBoost2) methods, and infer transcription-factor protein activity from regulons with VIPER and msVIPER. Covers the activity-not-edges paradigm, the undirected-association caveat, the DREAM5 wisdom-of-crowds and method-complementarity result, AUPRC-over-AUROC evaluation, and gold-standard incompleteness. Use when inferring a regulatory network from a bulk expression matrix, finding master regulators, or scoring TF activity from a signature. For single-cell motif-pruned regulons see scenic-regulons; for co-expression modules see coexpression-networks.

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Maps between gene identifier systems (Ensembl, Entrez, HGNC symbol, UniProt, RefSeq, MANE) using AnnotationDbi, biomaRt, mygene, pyensembl, and Ensembl REST. Encodes Ensembl version stripping with GENCODE _PAR_Y preservation, the Ziemann 2016 Excel autocorrect debacle and Bruford 2020 HGNC renames (SEPT*->SEPTIN*, MARCH*->MARCHF*, MARC*->MTARC*, DEC1->DELEC1), OCT4/POU5F1 alias resolution, biomaRt archive endpoints for release pinning, the `filters` (plural) gotcha, MANE Select for clinical reporting, cross-species orthology via Ensembl Compara / OMA / OrthoDB, and tx2gene construction for tximport. Use when converting gene IDs across systems, handling renamed symbols, building tx2gene, pinning to a specific Ensembl release for reproducibility, or mapping cross-species orthologs.

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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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Visualises RNA-modification data with transcript-feature metagene plots (Guitar GuitarPlot; MetaPlotR; deepTools computeMatrix scale-regions), peak-centred heatmaps (ComplexHeatmap; deepTools plotHeatmap), IP-vs-input paired browser tracks (log2 IP/input bigWig via deepTools bamCompare; pyGenomeTracks; Gviz; IGV/UCSC track hubs), DRACH sequence-logo plots (ggseqlogo; MEME), feature-distribution stacked bars, and volcano/MA plots for differential modification. Establishes stop-codon enrichment in the metagene plot as the biological QC anchor for any MeRIP dataset (Dominissini 2012; Meyer 2012). Use when producing the canonical metagene plot with stop-codon enrichment as a QC anchor, building paired IP/input genome-browser tracks at single-locus resolution, plotting peak-centred heatmaps clustered by condition, summarising peak distribution across transcript features, generating DRACH motif logos as sanity checks, rendering volcano plots of differential m6A, or reproducing the stop-codon enrichment plot.

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Reads, inspects, and writes Flow Cytometry Standard (FCS) files from conventional, spectral, and mass cytometry (CyTOF), and parses FlowJo/Cytobank/Diva workspaces. Covers FCS 2.0/3.0/3.1/3.2 internals ($PnE linear-vs-log, $DATATYPE, $SPILLOVER vs SPILL vs $COMP, $TIMESTEP), channel/parameter metadata, the silent linearize/truncate defaults, and R (flowCore, flowWorkspace, CytoML) plus Python (FlowKit, readfcs) readers. Use when loading flow or mass cytometry data, mapping detector channels to antibodies, extracting the event matrix, choosing a reader, or bridging FCS to the scanpy/AnnData ecosystem before preprocessing.

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Build genome-browser-style multi-track figures with pyGenomeTracks (config-driven), Gviz (R), and IGV batch screenshotting. Covers BigWig coverage tracks, BED/peak overlays, gene-model rendering, Hi-C matrix tracks, BedPE link arcs, spike-in-aware normalization, and the bamCoverage --normalizeUsing trap. Use when producing publication figures of genomic loci with stacked aligned tracks (coverage, peaks, genes, interactions) for ChIP-seq, ATAC-seq, RNA-seq, Hi-C, or generic locus visualization.

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Build OncoPrint and co-mutation matrix plots from somatic-variant cohorts using ComplexHeatmap, maftools, and comut.py with alteration-type stacking, sample ordering by mutational burden, mutual-exclusivity overlays, and clinical annotation tracks. Use when visualizing per-sample mutation patterns across recurrent driver genes, comparing alteration classes, or identifying mutually-exclusive / co-occurring driver pairs.

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Build UpSet plots to visualize set intersections beyond 4 sets (where Venn fails) using ComplexUpset (modern, ggplot2-grammar) or the unmaintained UpSetR, with explicit cardinality vs degree sorting, attribute panels, and query highlighting. Use when comparing overlap across many gene sets, peak sets, variant lists, or any set membership matrix where Venn diagrams become illegible.

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Tests genotype-environment associations and identifies adaptive loci while correcting for the four-confound landscape (structure, demography, background selection, sampling design) using LFMM2 with mandatory K via sNMF cross-entropy elbow (LEA 3), BayPass Core/AUX/C2/IS with Omega covariance matrix, RDA / pRDA for polygenic adaptation (Forester 2018; requires imputed genotypes), OutFLANK with trimmed FST null, pcadapt, gradient forests (Ellis-Smith-Pitcher 2012, NOT mis-cited Ellis-Manel), Capblancq & Forester 2021 RDA Swiss-army-knife, genomic-offset prediction with Lind & Lotterhos 2025 three-regime caveat, Lotterhos-Whitlock sampling optima, Wang & Bradburd 2014 IBD vs IBE, and Circuitscape + ResistanceGA. Use when identifying adaptive loci across gradients, choosing K for LFMM2, deciding among GEA methods, predicting maladaptation with the novel-environment caveat, distinguishing IBD vs IBE, or optimizing sampling design.

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Fits structural equation models to GWAS summary statistics using GenomicSEM (Grotzinger 2019), including common-factor models, confirmatory factor models, ESEM, common-factor GWAS with Q_SNP heterogeneity, multivariate Wald tests, and stratified GenomicSEM partitioned heritability. Reconciles results against MTAG multi-trait analysis. Handles sample overlap via the LDSC sampling-covariance matrix, identifies and resolves Heywood cases, and verifies model fit with CFI / RMSEA. Use when modeling latent genetic architecture across correlated traits, running multivariate GWAS on a shared factor, distinguishing factor-mediated from trait-specific SNP effects, or comparing GenomicSEM common-factor results against MTAG when both depend on accurate sampling covariance.

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Visualizes ChIP-seq data using deepTools (computeMatrix, plotHeatmap, plotProfile, bamCoverage, bamCompare), pyGenomeTracks (modern INI-driven track plots), Gviz (R browser-style), EnrichedHeatmap (ComplexHeatmap-based), ChIPseeker tag heatmaps, and IGV batch screenshots. Handles bigWig normalization choices (CPM, BPM, RPGC, spike-in scaled), bamCompare operations (log2 ratio, subtract) with SES scaling, k-means clustering of heatmaps for biological subgrouping, and spike-in-scaled tracks for global-shift experiments. Use when generating publication-quality ChIP-seq signal heatmaps, profile plots, genome-browser tracks, or comparing samples visually.

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Rapidly generate up to 25 distinct ad creative hypotheses for testing. Produces a matrix of angles (pain, benefit, social proof, urgency, curiosity, comparison) x formats (static, carousel hook, UGC-style, bold-text overlay) with headline, visual prompt, and rationale for each, then generates the visuals with any image tool. Use when the user wants "ad variations", "ad concepts", "creative testing batch", "give me 25 ads", or paid-social creative ideation. Part of the Creative Production set.

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Expert-level composites engineering covering fiber reinforced polymers, matrix materials, laminate theory, manufacturing processes, failure modes, and composite design.

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Expert-level linear algebra knowledge. Use when working with vectors, matrices, determinants, eigenvalues, linear transformations, vector spaces, inner products, decompositions, or applications in machine learning and physics. Also use when the user mentions 'matrix', 'determinant', 'eigenvalue', 'eigenvector', 'linear transformation', 'vector space', 'basis', 'orthogonality', 'SVD', 'PCA', 'least squares', 'null space', or 'rank'.

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Expert-level graph theory knowledge. Use when working with graph algorithms, network flows, matching, graph coloring, planar graphs, spectral graph theory, random graphs, or graph applications in computer science and networks. Also use when the user mentions 'shortest path', 'minimum spanning tree', 'network flow', 'bipartite matching', 'graph coloring', 'clique', 'independent set', 'vertex cover', 'planarity', 'graph isomorphism', 'adjacency matrix', or 'Laplacian'.

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Use when shaping brand voice — voice attributes, tone-by-context matrix, consistency review. Triggers on 'define our voice', 'why does our copy sound different on every surface'.

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Use when stakeholders pull a decision in different directions — frames each lens, builds a trade-off matrix, surfaces the cost of every choice — even if the user just says 'PO and ops disagree'.

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