「scoring」の検索結果

Annotate copy number variant segments with overlapping genes, dosage-sensitivity scores, cancer driver databases, population frequencies, and clinical-variant content. Covers bedtools/pybedtools interval intersection, AnnotSV comprehensive annotation and ranking, ClinGen haploinsufficiency/triplosensitivity scoring, gnomAD-SV/DGV frequency filtering, COSMIC Cancer Gene Census, and ClinVar overlap. Use when interpreting which genes a CNV affects, distinguishing the driver gene of a focal event from passengers, filtering against population CNVs, separating whole-gene from partial-gene overlap, or preparing CNVs for clinical classification.

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Designs and analyzes combinatorial CRISPR screens covering paired-Cas9 (Big Papi, Najm 2018), enhanced AsCas12a multiplex (enCas12a, DeWeirdt 2021), in4mer 4-guide-array Cas12a (Esmaeili Anvar N et al 2024 Nat Commun 15:3577) and the Inzolia paralog-pair library, paralog-buffering detection (Dede 2020 Genome Biol; Thompson 2021 Cell Reports 36:109597), genetic-interaction (GI) scoring as observed_double_LFC minus expected_additive_double_LFC, synthetic-lethal and synthetic-rescue interaction interpretation, the half-of-essentiality buffered by paralogs phenomenon, multiplex screen statistical analysis with MAGeCK MLE interaction terms, and the relationship to single-cell combinatorial Perturb-seq. Use when designing a paralog or pathway-pair screen, choosing between paired-Cas9 (Big Papi) and Cas12a multiplex (Inzolia), interpreting genetic interaction scores, identifying synthetic-lethal targets for drug development, or scaling beyond single-gene CRISPR screens.

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Identifies essential genes from CRISPR-Cas9 fitness screens using BAGEL2 (Kim & Hart 2021 Genome Med), a Bayesian classifier scoring per-gene Bayes Factors via log-likelihood ratios over per-sgRNA fold changes, calibrated against CEGv2 core-essentials (Hart 2017 G3, ~684 genes) and NEGv1 non-essentials (Hart 2014, ~927 genes). Covers the fc + bf + pr workflow, the linear-extrapolation improvement over BAGEL1 truncation, multi-target off-target correction, tumor-suppressor sensitivity (BAGEL2 detects enrichment), and BF-to-FDR calibration (BF >6 ≈ FDR 0.05 from Hart 2017). Use when classifying essential vs non-essential genes, calibrating BAGEL2 thresholds against PR curves, identifying tumor suppressors alongside essentials, comparing BAGEL2 hits to MAGeCK / drugZ, or generating publication-quality essentiality calls.

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Analyzes base-editing screens for variant function. Covers library design (Sanson 2020 GRACE, Hanna 2021 BRCA1/2 SNV scanning, Cuella-Martin 2021), CBE vs ABE chemistry choice (BE3/BE4 vs ABE7.10/ABE8.20/ABE8e), editing-window math (positions 4-8 from PAM-distal end, wider for ABE8e), bystander-edit quantification and the variant-call ambiguity it creates, sgRNA-efficiency filtering before hit calling, indel byproduct interpretation, the substitution-vs-indel diagnostic, variant annotation against ClinVar / COSMIC, and the Broad be-validation-pipeline. Use when designing a BE variant screen, choosing CBE vs ABE for a specific edit, interpreting bystander-confounded hits, distinguishing functional signal from indel artifact, integrating CRISPResso2 output with screen scoring, or deciding BE vs PE for SNV installation.

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Protein design quality control, filtering thresholds, and ranking guidance. Use this skill when: (1) Evaluating design quality for binding, expression, or structure, (2) Setting filtering thresholds for pLDDT, ipTM, PAE, (3) Checking sequence liabilities (cysteines, deamidation, polybasic clusters), (4) Creating multi-stage filtering pipelines, (5) Computing PyRosetta interface metrics (dG, SC, dSASA), (6) Checking biophysical properties (instability, GRAVY, pI), (7) Ranking designs with composite scoring. This skill provides research-backed thresholds from binder design competitions and published benchmarks.

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Workflow for enrichment testing, ranked-gene analysis, pathway scoring, and pathway-focused visualization across omics outputs.

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Chai-1 structure prediction for protein complexes and design validation. Use this skill when: (1) Predicting protein-protein complex structures, (2) Validating designed binders, (3) Predicting protein-ligand complexes, (4) Using the Chai API for high-throughput prediction, (5) Need an alternative to AlphaFold2. For QC thresholds, use protein-design-qc. For AlphaFold2 prediction, use alphafold2-multimer. For ESM-based analysis, use esm2-sequence-scoring.

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Quality control metrics and filtering thresholds for protein design. Use this skill when: (1) Evaluating design quality for binding, expression, or structure, (2) Setting filtering thresholds for pLDDT, ipTM, PAE, (3) Checking sequence liabilities (cysteines, deamidation, polybasic clusters), (4) Creating multi-stage filtering pipelines, (5) Computing PyRosetta interface metrics (dG, SC, dSASA), (6) Checking biophysical properties (instability, GRAVY, pI), (7) Ranking designs with composite scoring. This skill provides research-backed thresholds from binder design competitions and published benchmarks.

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Workflow for regulatory network inference, regulon scoring, perturbation-aware comparison, and network visualization.

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Binder design ranking using ipSAE (interprotein Score from Aligned Errors). Use this skill when: (1) Ranking binder designs for experimental testing, (2) Filtering BindCraft or RFdiffusion outputs, (3) Comparing AF2/AF3/Boltz predictions, (4) Predicting binding success rates, (5) Need better ranking than ipTM or iPAE. For structure prediction, use chai or alphafold. For QC thresholds, use protein-qc.

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Operate professional paid advertising across Google, Meta, YouTube, LinkedIn, TikTok, Microsoft, Apple, Amazon, Reddit, Pinterest, Snapchat, and X. Use for account intake, source-grounded audits, strategy, budget and measurement planning, creative production, experiments, reporting, monitoring, and explicitly approved campaign changes. Also trigger on PPC, paid social, retail media, attribution, tracking, landing pages, cross-platform conversion totals, negative keywords or search terms, beta-feature scoring, stale platform claims, API-token or credential setup, campaign deletion, and safe Claude Ads installation or uninstall.

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Persistent compounding memory for AI agents. 5 default MCP tools: session_start, session_end, remember, recall, check. Full surface (18 tools) available with --full flag. Two-verb model: inhale (session_start) and exhale (session_end). Correction-first memory with decision trail tracking, watch_for warnings, palace rooms with salience scoring, cross-project insight matching, same-day journal merging, ambient recall hooks. Local markdown only. Zero cloud, zero telemetry, Obsidian-compatible. Optional Supabase backend: when configured via `ar setup supabase`, recall() uses pgvector cosine similarity on OpenAI/Voyage embeddings instead of keyword search — same API, semantic understanding. Gracefully degrades to local search if not configured.

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Use when reviewing, auditing, scoring, or improving a real or synthetic MATLAB AI tutor transcript, tutoring prompt, generated lesson, exercise, feedback sequence, or skill behavior for MATLAB accuracy, active learning, assignment guardrails, feedback quality, debugging support, transfer prompts, and instructor-facing quality recommendations.

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Validates gate criteria before PRD lifecycle advancement by delegating to the readiness scoring pipeline (scripts/readiness.py). Returns a graduated PASS / WARN / BLOCK verdict with top blockers and their causal chain. Triggers before advancing from v0.X to v0.Y or explicit `/ghm-gate-check`.

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Iterative rubric-based evaluation and self-improvement loop. Builds a scoring rubric interactively, evaluates an artifact with multiple models in parallel (Codex, Gemini, Claude), then autonomously improves the artifact one criterion at a time until a score threshold is met or circuit breaker fires. "/rulph", "rubric evaluate", "rubric score", "multi-model evaluate", "score and improve", "evaluate and iterate", "grade this", "루브릭 루프", "채점 루프", "자율 개선", "개선 루프", "루브릭 평가"

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Analyze indexed codebases via graph database (neug) and vector index (zvec). Covers call graphs, dependencies, dead code, hotspots, module coupling, architecture reports, semantic search, impact analysis, bug root cause from GitHub issues, class diagrams (UML), and PR review (risk scoring, conflict detection, auto-merge candidates, labeling). Also covers creating, inspecting, and repairing a CodeScope index. Use for: code structure, who calls what, why something changed, similar functions, module boundaries, bug tracing, class relationships, PR risk/conflicts, or any question benefiting from a code knowledge graph. Applies when a `.codegraph` index exists in the workspace, or when the user wants to create one.

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Configure and use Elasticsearch for full-text search, custom analyzers, aggregations, and index management. Use when a user needs to design search mappings, write complex queries, build aggregation pipelines, tune relevance scoring, or optimize index performance for search workloads.

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Detect AI-generated text using rule-based analysis, LLM-as-judge scoring, and optional external APIs. Use when: auditing content for AI authorship, academic integrity checks, editorial review, SEO content audits.

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Run AI agent and LLM evaluations in CI/CD pipelines — automated quality gates that fail the build when AI output quality drops. Use when someone asks to "test my AI agent", "add evals to CI", "catch prompt regressions", "compare models", "evaluate LLM output quality", "set up AI quality gates", or "benchmark my agent before deploying". Covers eval frameworks (Cobalt, Promptfoo, Braintrust), LLM-as-judge scoring, threshold-based assertions, and GitHub Actions integration.

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Use when reviewing contracts, extracting key terms, identifying risks, or building contract analysis tools - covers NLP approaches, clause identification, and risk scoringUse when ", " mentioned.

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Acquisition is expensive. Retention is profitable. Customer success is the discipline of ensuring customers achieve their desired outcomes with your product - which leads to retention, expansion, and advocacy. This skill covers onboarding that activates, health scoring that predicts, retention plays that save, and expansion strategies that grow accounts. Use when "keywords, file_patterns, contexts, " mentioned.

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Keyword research and opportunity scoring via the DataForSEO Keywords Data and Labs APIs. Returns search volume, CPC, competition, intent classification, related keywords, and long-tail suggestions with a Keyword Score (0-100).

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AI Engineering Toolkit workflow skill. Use this skill when the user needs 6 production-ready AI engineering workflows: prompt evaluation (8-dimension scoring), context budget planning, RAG pipeline design, agent security audit (65-point checklist), eval harness building, and product sense coaching and the operator should preserve the upstream workflow, copied support files, and provenance before merging or handing off.

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Advanced Evaluation workflow skill. Use this skill when the user needs 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 and the operator should preserve the upstream workflow, copied support files, and provenance before merging or handing off.

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。