'apt' 검색 결과

Model gene-family birth-death dynamics across a species tree using CAFE5 (Mendes et al 2020 Bioinformatics 36:5516 gamma-distributed rate categories), CAFE5-error (annotation-error-aware), Count (Csurös 2010 ancestral state reconstruction), BadiRate (Librado 2012 likelihood + parsimony), DupliPHY-Family, and ALE/AleRax (for per-family DTL; see [[gene-tree-species-tree-reconciliation]]). Test lineage-specific gene-family expansions and contractions, distinguish biological dynamics from annotation artifacts, account for assembly fragmentation, identify functional enrichment in expanded / contracted families. Use when correlating gene-family changes with phenotype evolution, ranking lineages by adaptive gene-family-rate shifts, post-WGD dosage-balance analysis, or building Birth-death models from OrthoFinder presence/absence matrices.

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Performs subgroup and heterogeneous treatment effect (HTE) analyses for clinical trials. Covers Mantel-Haenszel pooling, Breslow-Day, interaction tests in regression, RERI for additive interaction, modern data-adaptive HTE methods (STEPP, SIDES, causal forests, X/R-learners), Bayesian shrinkage (Dixon-Simon, MAP, EXNEX), graphical multiplicity (Bretz-Maurer), and credibility frameworks (Sun BMJ, EMA 2019). Use when analyzing treatment effects across patient subgroups for regulatory submissions or precision-medicine claims.

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Detect positive (diversifying / episodic / pervasive) selection using codon dN/dS frameworks. Implements PAML codeml site models (M0/M1a/M2a/M7/M8/M8a), branch models, branch-site model A (Zhang 2005), and HyPhy methods (BUSTED, BUSTED-S, BUSTED-MH, BUSTED-PH, MEME, FEL, FUBAR, aBSREL, SLAC, RELAX, GARD, FUBAR-MH). Includes McDonald-Kreitman framework (asymptotic alpha, impMKT, polyDFE, DFE-alpha, GRAPES) for within-species + divergence inference, RERconverge for trait-correlated rate shifts, CSUBST for convergent substitution, and PhyloAcc for accelerated noncoding evolution. Use when testing adaptive evolution at codons, branches, or full gene; running GARD recombination pre-screen; controlling alignment-error and gBGC false positives; reconciling PAML vs HyPhy results; or performing genome-scale selection scans.

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Drafting and iterating sections of The Federated Harbor whitepaper — the third paper in the Curiositech sequence after Anchor (local identity) and Bonded Commons (local coordination), extending coordination across machines and administrative domains. Use when authoring a section, rewriting a section after a redteam/whitehat round, or composing a new chapter. NOT for marketing copy, NOT for the other two papers, NOT for production threat response.

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Principled action selection for autonomous agents using Expected Free Energy (EFE) under the Active Inference framework. Each candidate action is scored as G(n) = w_prag * (-E[p_n] * damping) + w_epist * (-Var[p_n] * novelty(n)), where agent beliefs are maintained as per-node Beta distributions and updated via Bayesian observation. Selection is a softmax over -gamma * G, making exploration an automatic consequence of uncertainty rather than a hardcoded epsilon. Precision weights w_prag and w_epist self-adapt via surprise history, shifting the agent between exploitation and exploration regimes without any manually tuned schedule.

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Architects the encryption, codec/transport, and premium-feature layer of a group video-calling product, on top of an already-chosen SFU topology. Covers E2EE patterns (Zoom leader-fan-out, Signal pairwise-fan-out, MLS/TreeKEM as in Discord's DAVE, Telegram's ledger consensus), the SFrame (RFC 9605) + WebRTC Insertable Streams mechanism letting an SFU relay encrypted frames it can't read, codec/transport choice (AV1/VP9 SVC vs. simulcast, Opus, congestion control, Media-over-QUIC, WHIP/WHEP), and which "premium" features (virtual backgrounds, live captions, recording, breakout rooms, spatial audio) survive E2EE vs. structurally can't. Use when adding E2EE to an SFU-based call, choosing a 2026 codec/SVC strategy, or deciding which features to disable under E2EE mode. NOT for call topology/platform choice (see webrtc-adhoc-video-chat, which this composes with). NOT for one-way broadcast (see managed-video-streaming-pipeline). NOT for the DM/group-chat text backend (see realtime-messaging-backend-architecture).

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Propose and safely admit immutable DAG revisions after failures, requirements, resource changes, or unresolved effects. NOT for mutating an executing graph in place or retrying an effect with unknown commit state.

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Threat-models protocols where authority, scarce resources, bonds, bounties, escrow, reputation, ordering, adjudication, or settlement create strategic incentives. Use to test attack utility, conservation, collusion, Sybil resistance, oracle capture, griefing, custody, liquidity, and residual risk. NOT for choosing payment or bond amounts without evidence, smart-contract code audit, legal or employment classification, DeFi trading, admitting workers, or settling claims.

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The intelligence layer of Jury-rig. Decomposes natural language tasks into proposed Hierarchical Task DAGs (HTDAGs), matches subtasks to skills, proposes wave and revision contracts, and expands nodes only when evidence supports a revised graph. Use for 'orchestrate', 'execute DAG', 'parallel agents', 'decompose task', 'coordinate skills'. NOT for single-skill tasks or simple linear workflows.

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Decides HOW to mutate a DAG when a node fails, quality is below threshold, or new information changes the plan. Selects from mutation strategies (add node, replace agent, fork paths, loop back, downgrade model) based on failure type, cost budget, and execution history. Activate on "DAG failed how to fix", "mutation strategy", "replan on failure", "adaptive DAG", "recovery strategy", "what to do when node fails". NOT for detecting failures (use dag-quality), executing mutations (use dag-planner), or runtime execution (use dag-runtime).

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Conduct Critical Decision Method (CDM) interviews to elicit expert reasoning strategies (L3 knowledge) from practitioners about specific challenging past incidents. Use when capturing expertise for skill development, preserving knowledge before practitioner departure, building post-incident learning artifacts, or investigating decisions in complex sociotechnical systems. Outputs structured incident reconstructions with cues, decisions, alternatives considered, and counterfactual analysis suitable for distillation into skills or training material.

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Build, debug, optimize, and deploy ComfyUI workflows for diffusion image, video, and audio generation. Activate on: ComfyUI workflow, ComfyUI custom node, ComfyUI API, ComfyUI Manager, KSampler, FLUX in ComfyUI, Wan 2.2 ComfyUI, Hunyuan video ComfyUI, LTX video ComfyUI, IPAdapter, ControlNet ComfyUI, Kijai wrapper, ComfyDeploy, RunComfy, ComfyUI security, GGUF quantization, TeaCache, Nunchaku, ACE-Step ComfyUI, F5-TTS ComfyUI, subgraphs ComfyUI. NOT for: A1111/Forge/Invoke (different UIs), training pipelines from scratch, non-diffusion ML models, or general image-API integrations (use generative-video-2026 / generative-music-audio / media-gen-deployment).

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Architecture-level decisions for putting a CDN in front of a web app's static assets, API responses, and file/media delivery: provider selection (hyperscaler vs. specialist $/GB), signed-URL / tokenized access for gating private content at the edge, cache invalidation strategy (versioned URLs vs. purge APIs), origin shield / tiered caching for high-miss-rate content, and CDN-layer geo-restriction. Use when deciding which CDN to put in front of a new or growing service, when private/paywalled files need edge delivery without an origin round-trip per request, or when purge/invalidation behavior is being designed rather than debugged. NOT for HTTP cache-control header syntax, Vary, stale-while-revalidate, or surrogate-key purge mechanics (see `cdn-cache-control-headers`); NOT for Cloudflare-specific product configuration once Cloudflare is already chosen (see `cloudflare`); NOT for video-specific transcoding, adaptive bitrate ladders, or streaming-protocol packaging (see `managed-video-streaming-pipeline`).

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Collage as a web design aesthetic — overlapping elements, mixed media, cut-out shapes, scrapbook layouts, and editorial magazine spreads adapted for the web. CSS techniques for layered compositions using z-index stacking, clip-path, mix-blend-mode, parallax layering, and grid-breaking layouts. Activate on 'collage web', 'editorial layout', 'magazine layout', 'overlapping elements', 'scrapbook', 'cut-out aesthetic', 'mixed media web', 'layered composition', 'grid-breaking', 'editorial web design', 'fashion website layout', 'David Carson'. NOT for photo collage/gallery grids (use collage-layout-expert), maximalist density (use maximalist-web-design), neobrutalism (use neobrutalist-web-designer).

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Render mathematically-faithful Turkish marbling (Ebru) and paper-marbling with closed-form coordinate-deformation maps — a drop is a radial outward push, a comb/tine is a decaying shear, all composed as homeomorphisms over colored region boundaries. No fluid solver, runs 60fps on a 2D canvas. Use when building a marbling/Ebru toy or generative-art renderer, implementing drop/comb/wave/swirl deformations, scripting traditional patterns (Battal, Gel-Git, Şal, Bülbül Yuvası), keeping combed edges crisp via adaptive resampling, modeling ox-gall shouldering for crisp ring-in-ring drops, or exporting high-DPI marbled prints. NOT for real fluid / Navier-Stokes simulation, metaball / alpha-blended "smoke" blob effects, raster image-processing filters, or non-marbling generative art.

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Own whether a multi-document product-architecture binder is internally consistent, complete against its stated customer/contingency/architecture coverage, and honest about which older product ambitions it has absorbed, superseded, deferred, contradicted, orphaned, or rejected. Use when running a binder Architect of Record pass, before an implementation chain cites a binder chapter as ready, when a proof-gate owner is missing, or when reconciling the binder against the older ambition corpus (website, plans, examples, ADRs). NOT for auditing a single Claude Skill bundle's structure or frontmatter (use skill-hygiene), rendering a single-PM accept/reject verdict on one finished deliverable (use port-daddy-user-surrogate-pm-review), or sequencing/stewarding a roadmap's sidequests once a gap or operator decision has been surfaced (use legible-roadmap-with-sidequests).

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Systematic methodology for eliciting, representing, and operationalizing expert cognitive skills—pattern recognition, situation assessment, mental simulation—from practitioners without requiring research training. Bridges academic rigor and practical usability.

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Design decisions for when and what sounds to use in web apps, mobile apps, and desktop native apps — plus how to create them with AI. Covers UI sound vocabulary (confirms, alerts, transitions, errors), platform conventions (iOS, macOS, Material), creating sounds with AI tools (ElevenLabs, AudioCraft, Stable Audio), Web Audio API for procedural sounds, haptic-audio pairing, and the psychology of satisfying vs. annoying UI sounds. Activate on 'app sounds', 'UI sounds', 'notification sound', 'sound design app', 'earcons', 'sonic branding', 'interaction sounds', 'feedback sounds', 'app audio', 'satisfying sounds'. NOT for professional audio engineering (use sound-engineer), Windows 3.1 retro sounds specifically (use win31-audio-design), music composition (use sound-engineer).

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Systematic methodology for eliciting, representing, and operationalizing expert cognitive skills—pattern recognition, situation assessment, mental simulation—from practitioners without requiring research training. Bridges academic rigor and practical usability.

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Design and build beautiful, accessible graphical interfaces — web, desktop (Electron/Tauri), and native (iOS/macOS/Android). Use for visual hierarchy and layout, color and theming (light/dark, semantic tokens, WCAG contrast), typography systems, motion and micro-interactions, accessibility, component systems and design tokens, responsive/adaptive layout, and platform-native idioms. The GUI counterpart to beautiful-cli-design. NOT for terminal/CLI output (use beautiful-cli-design) or API/data schemas.

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Track the full Toulmin epistemic ancestry of every claim produced by a multi-agent swarm. Each agent output is tagged with an argument chain (claim / data / warrant / relationship) derived from SwarmTracer spans and LineageEdge records, so operators can zoom into any sub-claim and see precisely which agents asserted it, what triggered each assertion, and how contradictions propagated or were synthesised away. The SwarmTracer pattern — wrapping the SwarmAgentExecutor to capture spans, record messages, and build a lineage graph — is the concrete runtime substrate. Argumentative lineage lifts that graph into the Toulmin vocabulary so reasoning provenance is both machine-queryable and human-interpretable.

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Design RL simulation sandboxes, trajectory datasets, QLoRA/LoRA adaptation plans, eval harnesses, and rollback unhooks for agents learning specific coding behaviors beyond the base model. Use when building or reviewing tool-use training loops, offline trajectories, reward functions, self-improvement harnesses, or Port Daddy agent behavior curricula. NOT for generic ML tutorials, full model training operations, or production deployment without eval gates and safety unhooks.

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Design or review a declared control-command profile and its verb/backend lifecycle matrix. Distinguish policy denial, unsupported capability, delivery acknowledgement, independently observed effect, and unknown outcome; bind authorization to principal, target, scope, current policy, expiry, and fencing epoch. NOT for claiming runtime correctness, proving an adapter from declarations, or approving a control-panel button without independent runtime evidence.

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Apply cognitive task analysis to expert work that depends on perceptual cues, branching judgment, and recurring monitoring loops. Use when decomposing expert capability into agent structure, simulation design, or validation interviews. NOT for ordinary step-by-step SOP capture or simple pipelines with no tacit cue layer.

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