리서치·학습 스킬

Add Apple Pencil drawing with PKCanvasView, PKToolPicker, PKDrawing serialization/export, stroke inspection, and PencilKit/PaperKit handoffs. Use when building drawing apps, annotation features, handwriting capture, signature fields, content-version-safe ink workflows, or Apple Pencil-powered experiences on iOS/iPadOS/visionOS.

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Add drawings, shapes, and a consistent markup experience using PaperKit. Use when integrating PaperMarkupViewController for markup editing, adding shape recognition, working with PaperMarkup data models, embedding markup tools in document editors, or building annotation features that need the system-standard markup toolbar. New in iOS 26.

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Calls germline small variants (SNPs and indels) from Oxford Nanopore and PacBio HiFi long reads with Clair3, a two-stage (pileup + full-alignment) deep-learning caller, selecting the chemistry- and basecaller-version-matched model, enabling read-based phasing, and benchmarking against GIAB with stratification. Covers why the model string is the experiment (no auto-detection, silent degradation on mismatch), why ONT homopolymer/STR indels are the residual error whole-genome F1 hides, and the somatic/trio/RNA boundary to the ClairS/Clair3-Trio family. Use when calling germline SNVs/indels from ONT or HiFi BAMs, choosing a Clair3 model, phasing variants, or benchmarking long-read calls.

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Detects m6A modifications from Oxford Nanopore direct-RNA-seq (DRS) signal using m6Anet (multiple-instance-learning over DRACH 5-mer signal). Covers the upstream pipeline (Dorado/Guppy basecalling -> minimap2 map-ont -> nanopolish eventalign -> m6anet dataprep -> m6anet inference), per-site vs per-read probability including the mod_ratio stoichiometry column, the DRACH-only constraint, minimum-coverage thresholds (20-50 reads/site), multi-condition comparison via xPore/Nanocompore/ELIGOS, Dorado native modification calling (RNA004, 2024+), and the cDNA-vs-DRS distinction (cDNA Nanopore CANNOT detect modifications). Use when calling m6A from ONT DRS without immunoprecipitation, choosing m6Anet vs xPore vs Nanocompore vs ELIGOS vs Dorado native, interpreting probability_modified vs mod_ratio vs per-read probabilities, deciding between m6Anet (known DRACH sites) and Dorado/Remora (genome-wide screening), pinning RNA002 vs RNA004 chemistry and basecaller versions, or troubleshooting eventalign/dataprep failures.

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Predicts protein-coding gene structures (exons, introns, UTRs) in eukaryotic genomes with BRAKER3 (RNA-seq + protein evidence), BRAKER1/BRAKER2, GALBA (protein-only), Funannotate (fungi), GeMoMa (homology projection), or Helixer/Tiberius (deep-learning ab initio). Covers the evidence-first tool decision, mandatory soft-masking, the training-set-quality-dominates principle, OrthoDB clade-partition selection, the one-isoform-per-locus and missing-UTR traps, merge/split errors, and reference bias against orphan genes. Use when annotating a newly assembled eukaryotic genome, choosing a gene-prediction pipeline based on available evidence, or diagnosing a poor annotation.

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Predict RBP binding from RNA sequence using deep learning models (RBPNet sequence-to-signal, RNAProt RNN, GraphProt2 GCN with structure, DeepCLIP, DeepRiPe multi-modal CNN) for variant-effect prediction, in silico binding-site discovery, model interpretation, and transfer learning from CLIP and RBNS datasets. Use when computational prediction of RBP binding from sequence is needed, evaluating variant effects on binding without further wet-lab experiments, comparing model performance, or training a custom model on ENCODE eCLIP data.

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Trains and applies base-resolution deep learning models on ChIP-seq / ChIP-nexus / CUT&RUN data. Uses BPNet (Avsec 2021 Nat Genet 53:354; soft motif syntax from ChIP-nexus), chromBPNet (Pampari A et al 2024 bioRxiv; bias-factorized base-resolution profiles), EnFormer (Avsec 2021 Nat Methods 18:1196; 196 kb input, ~100 kb effective receptive field), DeepSEA (Zhou 2015; multi-task CNN), and JASPAR 2026 deep-learning collection (1259 BPNet ChIP models). Performs in silico mutagenesis for variant-effect prediction, DeepLIFT/Grad attribution, and TF-MoDISco motif discovery from attribution scores. Use when predicting variant effects on TF binding, discovering soft motif syntax / cooperativity, integrating ChIP-seq with sequence-only predictions, or applying precomputed JASPAR Deep Learning models to new variants.

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Sequence-based deep learning for ATAC-seq using chromBPNet, BPNet, scBasset, or Enformer. Use when correcting Tn5 bias with neural networks beyond k-mer models, predicting per-base accessibility profiles, scoring in silico variant effects at GWAS or rare-variant SNPs, discovering motifs via DeepLIFT/TF-MoDISco from a trained model, or generating cell-type-specific accessibility predictions for unobserved cell states.

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Three modes for CS-conference papers (CVPR/ICCV/ECCV vision, ACL/EMNLP/NAACL NLP, ICLR/NeurIPS/ICML/AAAI ML). DIRECT-EDIT mode (common): the user describes a change in Chinese or English and the manuscript (LaTeX or Markdown) is edited directly through a CS-venue writing toolkit with author sign-off (use for 改这段 / 把中文想法写成 latex / polish / de-AI / translate / compress a passage). REVIEW mode (occasional, pre-submission): harden the paper through an adversarial courtroom review engine (N holistic domain reviewers / contestability routing / two-sided trial / three-way verdict / clerk-converged multi-round loop) with consensus-gated, author-signed revisions (use for review / critique / 审稿 / 评审 / mock-review). AUTO mode (unattended, opt-in via /goal): run the review-revise loop toward a verifiable goal, applying safe fixes under a drift-bounded policy and queueing risky ones. Resolves all inputs at runtime, no hardcoded paths. Not a from-scratch drafter (use ml-paper-writing) and not an official-venue rebuttal.

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Report the compatibility redirect to `ap-worker`; this retired role cannot perform new work.

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Use when the user needs multi-source research with citation tracking, evidence persistence, and structured report generation. Triggers on "deep research", "comprehensive analysis", "research report", "compare X vs Y", "analyze trends", or "state of the art". Not for simple lookups, debugging, or questions answerable with 1-2 searches.

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This skill should be used when user asks to "improve my mAP", "why is my model overfitting", "my training is diverging", "read my results.csv", "interpret my training curves", "my AP50 is good but AP50-95 is bad", "my recall is low", "how do I pick learning rate", "which augmentations should I use", "should I use a bigger model", "tune hyperparameters", or asks how to train YOLO26 for detection, instance or semantic segmentation, pose, OBB, classification, or depth.

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This skill should be used when user asks to "fetch overleaf review comments", "address overleaf reviews", "apply overleaf comments", "review my overleaf paper", "sync overleaf feedback to local", "what comments are on my overleaf doc", or wants to act on Overleaf reviewer feedback in a local git-tracked LaTeX repo.

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This skill should be used when the user asks to "set up paper search", reports "paper-search command not found", wants to "replace paper search MCP", or needs help with paper search credentials.

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This skill should be used when the user asks to "search for papers", "find research papers", "search arXiv", "search PubMed", "look up a DOI", "download a paper", "search IEEE", or "search Scopus".

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Use when researching social posts, creators, reactions, or trends. Jev ranks discovery cards and decides when opened, source-linked evidence is enough for a bounded report.

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Create or update a product-discovery SPEC (requirements doc) for user review. Use when turning RESEARCH findings plus user intent into a reviewable requirements artifact before INNOVATE/PLAN.

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Fast codebase scouting using shell search and optional parallel research agents. Use for file discovery, task context gathering, and quick scoped searches across directories.

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Loop: find gaps → fix → repeat until agents find no gaps or a metric goal is hit. Shared loop primitive for PVL, EVL, and standalone quality runs.

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Gather external knowledge the spec needs and distill it into §R — the durable research log — so build grounds in facts instead of hallucinating library behavior. Each finding cites a source; unsourced claims are flagged, never written as fact. Triggers when a spec decision hinges on a library/API/best practice the agent is unsure of, when the user says "research this", "what's the best lib for…", "check current best practice", or invokes /ck:research. Defers the §R write to the spec skill.

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Adversarial senior review of the spec before any code is written. Constructs a skeptical reviewer whose authority comes from the codebase, §R research, and live best-practice — then tries to REFUTE the spec, not rubber-stamp it. Every finding cites evidence (file:line or source); unverifiable ones are flagged. Survivors harden §V; the run ends in an explicit go / no-go gate. Triggers before building anything high-blast-radius, when the user says "review the spec", "red-team this", "is this plan sound", "senior review", or invokes /ck:review.

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Assists in writing high-quality content by conducting research, adding citations, improving hooks, iterating on outlines, and providing real-time feedback on each section. Transforms your writing process from solo effort to collaborative partnership.

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Turn books, PDFs, slides, documents, web pages and text into a source-grounded knowledge base, interactive learning HTML and Markdown in English or Chinese. Use for learning, summaries, explanations, review, quizzes, relationship maps, saving reusable methodology files, retrieving or comparing accumulated methods, and applying them to a real problem. 将材料转为可追溯知识库与交互学习页，支持中英文、关系图、方法论保存/检索/比较及应用；区分材料依据、推断与外部核验。

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Produce a periodic review of a second-brain vault: what was added, which topics are growing, what contradicts what, which questions are still open, and what is worth reading next. Use this skill whenever the user asks for a weekly or monthly review, asks what changed in their vault, what they have been learning about lately, or what they should look at next, and when a scheduled review task fires. Do NOT use for structural linting, for ingesting sources, or for answering a specific factual question.

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