「candidate」の検索結果

Experiment design reference for problem-class framing, Minimum Viable Experiment coaching, hypothesis formation, vetting and red flags, and experiment readiness. Use when translating a stated business outcome into candidate data-science problem classes, or when framing, vetting, scoping, or evaluating an experiment of any kind, including data feasibility, architecture, LLM, performance, use-case, UX, prototyping, and hardware experiments.

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Read-only evo run reporting. Use when the user invokes /evo:report, asks what happened overnight, asks what improved recently, asks for the best/frontier candidates, asks for a quick score chart without opening the dashboard, or wants the scatter plot in chat output. Never run benchmarks, gates, Slurm commands, evo run, or ad-hoc verification scripts for report requests.

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Gated checklist to choose or review a library, framework, storage, data format, model, build-vs-buy or architecture. Run favorites-search before external research when installed. Compare candidates and trade-offs; select within authorization or return user-owned choices. Use for 用哪个 / 选什么框架 / 要不要自建 / A 还是 B / 这个方案行不行 and before committing to one. Research reports → deep-research.

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Build a candidate's research brief on a company before an application or interview. Use when asked to research a company for a job, prep a company brief before an interview, or understand a prospective employer fast. Produces a one-page brief — what they do & how they make money, recent news & trajectory, product & competitors, likely challenges, culture signals, and smart questions to ask.

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Review a bill of materials for cost, risk, and supply exposure — cost rollup, top-10 cost drivers, single-source and EOL risk, MOQ vs forecast mismatch, cost-down candidates, and tariff/logistics sensitivity. Use when asked to review a BOM, find cost-down opportunities, check component sourcing risk, or sanity-check BOM cost against target. Produces a structured BOM review with a cost driver Pareto, risk flags per line, and a prioritised cost-down list.

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Help users design and execute a high-signal interview process that prioritizes real-world performance over superficial charisma or pedigree.

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Use when opening the formal release vote for a Struts release candidate on any maintenance line (6.x, 7.x) - composing and drafting the [VOTE] Apache Struts X.Y.Z mail to dev@ once the Version Notes page, GitHub release and staged artifacts are published.

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Use when preparing, updating, or reviewing the release documentation for a Struts release or release candidate on any maintenance line (6.x, 7.x) - the Version Notes page on the cwiki, its Migration Guide entry, the GitHub release notes, and the test-build announcement mail.

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Detect Server-Side Template Injection (SSTI) vulnerabilities in a codebase using a three-phase approach: recon (find template rendering sites that use dynamic strings), batched verify (trace user input to those sites in parallel subagents, 3 candidates each), and merge (consolidate batch results). Requires sast/architecture.md (run sast-analysis first). Outputs findings to sast/ssti-results.md. Use when asked to find SSTI or template injection bugs.

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Detect GraphQL injection vulnerabilities in a codebase using a three-phase approach: recon (confirm GraphQL usage and find unsafe operation document assembly sites), batched verify (trace user input to those sites in parallel subagents, up to 3 candidate sites each), and merge (consolidate batch results). Requires sast/architecture.md (run sast-analysis first). Outputs findings to sast/graphql-results.md. If no GraphQL technology is found in Phase 1, later phases are skipped. Use when asked to find GraphQL injection, unsafe GraphQL document construction, or operation string injection bugs.

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CP-7 retrospective: audit checkpoints, evidence quality, action items, and harvest candidates. Closes the V-model cycle and feeds the next run. Use via /retro after ship, escalate, or significant session.

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Designs and ranks guide RNAs (sgRNAs) for CRISPR-Cas9/Cas12a gene knockout by scanning a target for PAM sites (NGG SpCas9, NNGRRT SaCas9, TTTV Cas12a, NG SpCas9-NG, near-PAMless SpRY), enumerating candidate spacers, applying hard filters (Pol-III TTTT terminator, 5' G, GC), ranking on-target activity with the context-appropriate model (Rule Set 2/Azimuth for U6/lentiviral, CRISPRscan for T7/embryo, DeepHF for high-fidelity variants, DeepCpf1 for Cas12a), and predicting the indel/frameshift outcome (Bae out-of-frame score, inDelphi, FORECasT, Lindel). Use when selecting sgRNAs to knock out a gene, choosing a nuclease/PAM for a constrained locus, picking which exon to target, or shortlisting guides before an off-target check. Off-target specificity, base/prime editing, and HDR donors are separate skills.

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Identify tumor neoantigens from somatic variants with pVACtools (pVACseq/pVACfuse/pVACbind/pVACvector/pVACview) for personalized cancer vaccines and checkpoint biomarkers. Encodes the field's hard truth that binding prediction is the easy, near-solved part and single-digit-percent PPV lives downstream — so it centers clonality/CCF, HLA LOH (the silent invalidator), expression, proximal-variant phasing, agretopicity/foreignness quality, and the predicted->presented->immunogenic validation tiers. Use when nominating vaccine targets, ranking neoantigens, or building a tumor-to-candidate pipeline. Binding details in mhc-binding-prediction; ranking in immunogenicity-scoring.

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Infer or annotate TCR antigen specificity by unsupervised clustering (TCRdist/tcrdist3, GLIPH2, clusTCR, GIANA) and database lookup (VDJdb, IEDB, McPAS-TCR), and rank candidates with supervised predictors (ERGO-II, NetTCR-2.x, pMTnet) under explicit caveats. Encodes the central truth that general TCR-epitope prediction for UNSEEN epitopes essentially does not work (collapses to near-random; IMMREP22, Grazioli 2022) because labeled data is dominated by a few immunodominant epitopes and there is no true negative set — so clustering for discovery is the honest task and de-novo binding needs wet-lab validation. Use when annotating TCR specificity or grouping a repertoire. Epitope/MHC context lives in mhc-binding-prediction.

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Analyzes CRISPR drug-modifier (chemogenomic) screens with drugZ (Colic et al. 2019 Genome Med), a bidirectional Z-score method that identifies synthetic-lethal sensitizing genes and resistance-conferring suppressor genes from vehicle vs drug comparisons. Covers vehicle-anchored design (not Day-0), the bidirectional Z math giving greater sensitivity to small-effect hits than MAGeCK / STARS / edgeR / RIGER on drug screens, per-gene sumZ and normZ, synth (sensitizer) vs supp (suppressor) FDR, multi-dose handling, integration with control sgRNAs, and comparison with MAGeCK MLE with dose covariate. Use when running a drug-modifier CRISPR screen, identifying sensitizing or resistance genes for a drug candidate, choosing drugZ vs MAGeCK MLE for chemogenomic analysis, troubleshooting low-effect drug screens where MAGeCK lacks sensitivity, or designing a drug-screen layout (vehicle vs drug arms).

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Prioritizes rare-disease variants from trio/quad WES/WGS with de novo (DeNovoGear, Triodenovo), compound-heterozygous phasing (WhatsHap), mosaic VAF tiering, phenotype-driven ranking (Exomiser, Phen2Gene, AMELIE), ClinGen gene-disease validity gating, and ACMG SF v3.2 secondary findings reporting. Use when running diagnostic exome / genome pipelines, identifying candidate Mendelian disease genes, screening for incidental findings, or auditing VUS reclassification cycles. The ACMG/AMP classification framework (PVS1 decision tree, Pejaver PP3/BP4 calibration, Tavtigian point system) is in clinical-databases/acmg-classification.

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Annotates ChIP-seq peaks to genomic features, nearest genes, ENCODE candidate cis-regulatory elements (cCREs), and regulatory domains. Uses ChIPseeker (R), HOMER annotatePeaks.pl (CLI), pyranges (Python), GREAT/rGREAT (regulatory domain gene-set enrichment), ChIP-Enrich (locus-length-adjusted), ENCODE SCREEN cCRE classification (PLS/pELS/dELS/CA-CTCF/CA-H3K4me3), and ENCODE-rE2G for cell-type-specific enhancer-gene linking. Handles nearest-TSS vs host-gene ambiguity, promoter window definition, and feature priority. Use when assigning genomic context to peaks, linking enhancer peaks to target genes, classifying peaks against ENCODE cCRE registry, or running gene-set enrichment on peak-associated genes.

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Builds and applies 3D pharmacophore models using RDKit Pharm3D, the apo2ph4 receptor-based workflow (Heider et al. 2023), Pharmer / Pharmit for search, and PharmacoForge for protein-pocket-conditioned pharmacophore generation (Flynn et al. 2025), covering ligand-based pharmacophores from active-set alignment and receptor-based pharmacophores from binding-pocket geometry. Explicitly handles feature types, geometric tolerances, partial matching, and pharmacophore-based virtual screening. Use when identifying scaffold-hopping candidates, building shape-and-feature search queries, or transferring SAR across chemotypes.

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Performs structure-based virtual screening using AutoDock Vina, SMINA, GNINA (CNN scoring), and DiffDock-L hybrid workflows with explicit choice rules across rigid vs flexible docking, cross-docking vs self-docking, binding-site detection (P2Rank, fpocket), receptor preparation (PDB2PQR, PROPKA), ligand preparation (meeko, OpenBabel), and ultralarge-library screening (ZINC22, Enamine REAL). Use when screening chemical libraries against a protein target to find candidate binders, ranking docking poses, or selecting a docking workflow for a specific scenario.

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Resolves GWAS associations to candidate causal variants and credible sets via SuSiE, susie_rss, FINEMAP, CAVIAR, DAP-G, PAINTOR, PolyFun, SuSiEx, MultiSuSiE, and FOCUS. Use when narrowing a GWAS lead SNP to a 95 percent credible set, choosing between in-sample and reference LD, calibrating non-sparse loci with SuSiE-inf or FINEMAP-inf, integrating functional priors via PolyFun, fine-mapping across ancestries with SuSiEx, diagnosing LD mismatch via estimate_s_rss and kriging_rss, handling HLA or long-range LD, or feeding credible sets into coloc.susie for colocalization.

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Performs gene-level association from GWAS summary statistics via genetically predicted tissue expression using FUSION, PrediXcan, S-PrediXcan, S-MultiXcan, UTMOST, MOSTWAS, kTWAS, EpiXcan, TIGAR-V2, and probabilistic fine-mapping with FOCUS and MA-FOCUS. Use when running TWAS from GWAS sumstats, prioritising candidate causal genes from a GWAS lead locus, picking single-tissue vs cross-tissue models, identifying LD-induced TWAS false positives, choosing ancestry-matched prediction weights, fine-mapping co-regulated TWAS hits, or triangulating TWAS with cis-eQTL Mendelian randomization and colocalization to nominate a causal gene.

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Viking Search tuning for specified policy directions. Use this when the user provides specific queries, a type of query, or a business policy direction, and asks to boost, suppress, or fix a class of search results through request-parameter passthrough. You must only perform read-only baseline evaluation and request-level candidate testing; do not modify search scenes, app config, dictionaries, recommend scenes, or primary recall parameters.

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Evaluate ecommerce price candidates using unit economics, historical observations, elasticity analysis, scenario modeling, and controlled experiments. Use when a seller asks what price to test, how price changes could affect contribution or revenue, how to estimate elasticity, how to optimize a bundle or tier, or how to design a price experiment across Amazon, Shopify, TikTok Shop, Walmart, eBay, or other channels. Do not claim a proven optimal price without sufficient clean data, and do not change live prices without explicit authorization.

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Build and risk-screen a compact role-based method shortlist for a mathematical-modeling subquestion. Use after problem framing and data profiling, before model code generation, to propose a main candidate, a usable baseline, and at most one conditional fallback without padding the pool.

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