“skill evolution”的搜索结果

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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Resolve subclonal copy number, whole-genome doubling, and copy-number tumor evolution from bulk sequencing with Battenberg, TITAN, and MEDICC2. Covers clonal versus subclonal copy-number states, haplotype phasing for subclonal resolution, cancer cell fraction, whole-genome-doubling detection and timing relative to mutations, mirrored subclonal allelic imbalance, and copy-number phylogenies. Use when a tumor is heterogeneous and bulk data shows non-integer copy number, when calling subclonal CNAs, detecting or timing whole-genome doubling, reconstructing copy-number evolution, or deciding between Battenberg and TITAN.

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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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Argentine Supreme Court citation network analysis using JurisRank — a peer-reviewed PageRank algorithm with temporal decay for measuring jurisprudential authority. Ranks precedents by citation influence, traces doctrinal evolution, and detects constitutional drift. Published methodology: JCLLT (DOI: 10.47852/bonviewJCLLT62027951). Activate with: which cases to cite, rank precedents, case authority, doctrinal evolution, Argentine Supreme Court, CSJN jurisprudence, citation network, leading case, legal research Argentina.

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Agent self-evolution system. Collects signals from user feedback, stores execution trajectories (golden + correction pairs), analyzes patterns, proposes mutations to workspace files, and generates HTML reports. Trigger with "/evolve" or when the user asks to improve agent behavior. Also use when the user says "remember this pattern", "don't do X again", or "that was a good approach, save it".

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Python framework for single- and multi-objective optimization with evolutionary algorithms. Define vectorized objectives and constraints; solve with NSGA-II, NSGA-III, MOEA/D, GAs, or differential evolution. Analyze Pareto fronts, visualize trade-offs, customize operators and callbacks. For engineering design, hyperparameter search, and conflicting objectives. Alternatives: scipy.optimize (single-objective, gradient), platypus, jMetalPy (Java).

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Analyze data evolution patterns in construction organizations. Assess digital maturity and data strategy for construction companies

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Applies the reasoning, principles, and frameworks of Jürgen Schmidhuber (LSTM co-inventor and deep learning pioneer). Reach for this skill whenever tackling problems involving sequence learning, artificial curiosity, intrinsic motivation, reinforcement learning architectures, or predicting long-term technological and cosmic evolution. Use this when discussing AGI timelines, the history and attribution of AI breakthroughs, data compression as learning, or when designing autonomous agents that must set their own goals. Trigger this skill for topics like recurrent neural networks, algorithmic information theory, open-source AI democratization, and evaluating true existential risks versus media hype.

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Applies the reasoning, architectural principles, and AI philosophy of Christopher Manning (natural language processing expert, Stanford University, director of Stanford AI Lab). Use this skill whenever you are discussing natural language processing, LLM architecture, AI research strategy, cognitive science, or the evolution of machine learning. Trigger this skill for questions about AGI timelines, academic vs. industry research trade-offs, linguistic structure in neural networks, modularity in AI design, or evaluating true intelligence versus mere memorization. Channel his pragmatic focus on domain science, adaptability, and competing on ideas rather than raw compute.

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Analyze Chinese notes, articles, manuscripts, and digital card-box material with FIRE 2.0: Full-D numbering, Index keyword webs, Route thinking paths, and Evolution over time. Use when Codex needs to prepare material for semantic search, turn temporary notes into permanent or project notes, build table-of-contents/index/search structures, create compact Chinese FIRE cards, or maintain this skill's original discussion thread provenance.

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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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Version REST and GraphQL APIs. Use when a user asks to version an API, handle breaking changes, implement API deprecation, manage multiple API versions, or design an API evolution strategy.

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You are an expert in Airbyte, the open-source data integration platform with 300+ pre-built connectors. You help developers sync data from SaaS tools, databases, and APIs into data warehouses and lakes — handling incremental syncs, CDC (Change Data Capture), schema evolution, and error recovery for production data pipelines.

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Applies the reasoning, principles, and frameworks of Jürgen Schmidhuber (LSTM co-inventor and deep learning pioneer). Reach for this skill whenever tackling problems involving sequence learning, artificial curiosity, intrinsic motivation, reinforcement learning architectures, or predicting long-term technological and cosmic evolution. Use this when discussing AGI timelines, the history and attribution of AI breakthroughs, data compression as learning, or when designing autonomous agents that must set their own goals. Trigger this skill for topics like recurrent neural networks, algorithmic information theory, open-source AI democratization, and evaluating true existential risks versus media hype.

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Applies the reasoning, architectural principles, and AI philosophy of Christopher Manning (natural language processing expert, Stanford University, director of Stanford AI Lab). Use this skill whenever you are discussing natural language processing, LLM architecture, AI research strategy, cognitive science, or the evolution of machine learning. Trigger this skill for questions about AGI timelines, academic vs. industry research trade-offs, linguistic structure in neural networks, modularity in AI design, or evaluating true intelligence versus mere memorization. Channel his pragmatic focus on domain science, adaptability, and competing on ideas rather than raw compute.

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Stellar structure and life cycles from birth to endpoint. Covers the Hertzsprung-Russell diagram, hydrostatic equilibrium, main-sequence physics and the mass-luminosity relation, nuclear fusion stages (pp-chain, CNO cycle, triple-alpha), nucleosynthesis, post-main-sequence evolution through red giants and the horizontal branch, and stellar endpoints — planetary nebulae, white dwarfs and the Chandrasekhar limit, supernovae, neutron stars, and black holes. Use when placing a star on the HR diagram, estimating its lifetime, predicting its fate from its mass, or teaching how a star lives and dies.

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Self-evolution workflow for the agent. Before substantive work, recall past outcomes from evolution memory; while editing, detect improvement signals; at task end, record the outcome; when reusable, distill or search the EvoMap network for proven genes/capsules. Use when the user starts non-trivial work (a feature, a fix, a refactor) or asks the agent to "evolve", "learn from this", or "remember how this went".

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Repair or extend CodyMaster skills with a three-mode loop: FIX, DERIVED, and CAPTURED, grounded in current repo tooling.

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Monitors private credit market evolution with AUM growth, competitive dynamics, and spread convergence with broadly syndicated markets. Use when analyzing private credit trends, tracking market evolution, or assessing competitive positioning.

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Spring Data JPA entity design, repository patterns, query methods, JPQL, Flyway/Liquibase migrations, and N+1 avoidance. Apply on Spring Boot projects with spring-boot-starter-data-jpa. Pairs with spring-boot-plugin:spring-conventions and java-foundation:java-conventions. Use this skill to: - Design JPA entities with proper annotations, ID strategy, and lazy loading. - Write JpaRepository interfaces with derived query methods and JPQL @Query. - Avoid N+1 queries using @EntityGraph or JOIN FETCH. - Manage schema evolution with Flyway or Liquibase. - Project query results with Spring Data Projections and DTOs. Do NOT use this skill for: - Service or controller patterns — see spring-boot-plugin:spring-conventions. - Build tool setup — see java-foundation:build-tooling. - Test slices (@DataJpaTest) — see java-foundation:jvm-testing.

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AI向けマークダウンドキュメント（SKILL.md、AGENTS.md、.agent/*.md など）の健全性チェックと修正を支援するスキル。「ドキュメントの整合性を確認」「SSOT違反を探す」「スキル定義をメンテしたい」「PRの概要を更新したい」と依頼されたときに使用する。

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"Apply Complex Adaptive Systems theory to analyze phenomena exhibiting emergence, self-organization, co-evolution, and edge-of-chaos dynamics. Use this skill when the user needs to understand why a system behaves unpredictably despite known components, model agent-based interactions that produce emergent outcomes, analyze fitness landscapes, or when they ask 'why does this system behave in ways no one designed', 'how do local interactions create global patterns', or 'why do small changes sometimes cause massive system shifts'.".

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Run a Meta-Harness-style optimization loop NATIVELY — automatically search over the scaffolding around a FIXED base model (memory, retrieval, context construction, prompt templates, summarization, tool-selection logic) by proposing candidate variants, scoring each on a cheap deterministic eval, and keeping a Pareto frontier of quality vs cost — using native Agent / Workflow / loop tools instead of a standalone Python harness. Use this whenever the user wants to optimize, evolve, tune, distill, or search over a harness, scaffold, prompt system, memory or retrieval policy, context-assembly code, or summarizer while keeping the model fixed; whenever they mention Meta-Harness, harness optimization, scaffold evolution, automatic prompt/memory optimization, an evolutionary or Pareto search over candidate implementations, or "make the harness/agent better without retraining"; and whenever the gain must come from the code AROUND the model rather than the model weights. Reproduces the Meta-Harness paper's method natively, with no claude_wrapper.py and no metered solver API.

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A self-evolution engine for AI agents. Analyzes runtime history to identify improvements and applies protocol-constrained evolution. Communicates with EvoMap Hub via local Proxy mailbox.

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