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Triage an incoming insurance claim: check the coverage trigger against policy wording, band severity and complexity, screen for fraud indicators, set a first-pass reserve range, and route with an SLA. Use when asked to triage a claim, review a first notice of loss (FNOL), assess a new claim, decide fast-track vs adjuster routing, or screen a claim for SIU referral. Produces a structured triage note with coverage view, severity band, indicator screen, reserve range, and a routing recommendation.

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Produce a matched Chinese and English CV (中英文简历) from one set of facts: each version follows its own conventions rather than a literal translation, with names, titles, dates, education and company names rendered correctly in both. Use when asked for a Chinese and English resume, translate my CV into Chinese, 中英文简历, 英文简历, or apply to a foreign company in China or a Chinese company abroad. Produces the Chinese CV, the English CV, a consistency table proving the facts match, and a glossary of the terms chosen.

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Database specialist for SQL, NoSQL, and vector database modeling, schema design, normalization, indexing, transactions, integrity, concurrency control, backup, capacity planning, data standards, anti-pattern review, and compliance-aware database design. Use for database, schema, ERD, table design, document model, vector index design, RAG retrieval architecture, migration, query tuning, glossary, capacity estimation, backup strategy, database anti-pattern remediation work, and ISO 27001, ISO 27002, or ISO 22301-aware database recommendations.

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Parameter-efficient fine-tuning for LLMs using LoRA, QLoRA, and 25+ methods. Use when fine-tuning large models (7B-70B) with limited GPU memory, when you need to train <1% of parameters with minimal accuracy loss, or for multi-adapter serving. HuggingFace's official library integrated with transformers ecosystem.

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Battle-tested PyTorch training recipes for all domains — LLMs, vision, diffusion, medical imaging, protein/drug discovery, spatial omics, genomics. Covers training loops, optimizer selection (AdamW, Muon), LR scheduling, mixed precision, debugging, and systematic experimentation. Use when training or fine-tuning neural networks, debugging loss spikes or OOM, choosing architectures, or optimizing GPU throughput.

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Write and edit project docs (README/markdown) as a glossary of principles, not a mirror of the code. Use when creating or revising a README; when a doc enumerates exact scenes, scenarios, helpers, class ids, file lists, or command/flag matrices the code already holds; when trimming narrative or changelog out of a doc; or when deduplicating overlapping docs and wiring a root doc to its sub-docs.

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Translate PDF documents with BabelDOC while retaining layout, figures and formulas; supports bilingual output, custom glossaries, domain terminology and local processing with configurable translation providers. Use for translated PDFs, not merely summaries or plain text extraction.

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Use after first-run for ongoing modpack maintenance: update/install KB packs, author or register custom/mod KB packs, maintain localization glossary KBs for translator use, prune KB cache, health-check the environment, version-pin KB/tooling, or handle recurring BGS modding environment care.

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Audit a repo's agent context — CLAUDE.md files, codebase docs, skills, and tool/MCP designs — against Anthropic's Claude 5 context-engineering guidance ("unhobbling": Anthropic cut ~80% of Claude Code's system prompt with no eval loss). Finds overconstraint, conflicting instructions, redundancy, stale facts, and missing "unknown knowns"; produces a scored findings report with concrete rewrites, then applies approved fixes. Use when someone says "audit my CLAUDE.md", "context audit", "unhobble this repo", "review our agent docs/skills/tools", or after upgrading to Claude 5-generation models.

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Research a specific competitor across their website, reviews, ads, social presence, and pricing — then produce a structured sales battlecard with positioning traps, objection handlers, landmine questions, and win/loss themes. Chains web research, review mining, and ad intelligence. Use when sales needs competitive ammo or when entering a new market with established incumbents.

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Detects A/B chromatin compartments from balanced Hi-C contact matrices via eigenvector decomposition of the distance-normalized, Pearson-correlated cis matrix with cooltools (eigs_cis), then orients (phases) the compartment eigenvector against a GC or gene-density track so the active (A) sign is not arbitrary. Covers the eigenvector-is-a-choice problem (per-arm view_df to remove the centromere gradient; picking the eigenvector by max correlation with activity, not by eigenvalue), GC phasing with bioframe.frac_gc, resolution choice (100kb-1Mb), saddle plots and saddle_strength for compartmentalization strength, the cohesin-loss-strengthens-compartments result, subcompartments (SNIPER/Calder/dcHiC), and cross-condition compartment switching. Use when calling A/B compartments, computing E1/eigenvectors, phasing the eigenvector, building saddle plots, choosing a compartment resolution, quantifying compartment strength, or comparing compartmentalization across conditions.

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Processes eDNA metabarcoding from raw paired-end reads to species tables, navigating ASV (DADA2, UNOISE3) vs OTU (swarm v2) decision (Callahan 2017 vs Schloss multi-copy-16S critique), marker/primer choice (Leray COI, MiFish 12S, 515F/806R 16S, ITS2) with primer-specific bias, OBITools3 v3 command-name break (obi stats plural; .tar.gz taxonomy), tag-jumping with dual-indexing (Schnell 2015; NovaSeq 10x MiSeq), decontam as screening-not-classifier (Davis 2018), read-counts-not-abundance critique (Lamb 2019), site-occupancy modeling (Ficetola 2015), Naive-Bayes calibration limits (Bokulich 2018), and eDNA decay (Strickler 2015). Use when going from raw eDNA FASTQ to species tables, picking marker + denoising pipeline, deciding whether read counts represent abundance, applying occupancy modeling, configuring OBITools3 v3, or interpreting decontam output. Not for clinical 16S microbiome (see microbiome/amplicon-processing).

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Detect horizontal gene transfer (HGT / LGT) using compositional methods (GC%, codon usage, tetranucleotide z-scores via SIGI-HMM, AlienHunter, IslandViewer 4, IslandPath-DIMOB), phylogenetic-incongruence methods (AvP, HGTphyloDetect, ALE / GeneRax / AleRax reconciliation, RANGER-DTL), and BLAST-distribution methods (HGTector v2, DarkHorse, Alien Index). Use when screening prokaryote genomes for genomic islands and HGT events, distinguishing HGT from incomplete lineage sorting / differential gene loss / hybridization, mapping donor lineages via phylogenetic placement, separating eukaryotic HGT from contamination, ruling out gBGC as a false signal, or quantifying DTL rates with ALE/GeneRax on bacterial trees.

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Project gene annotations across genomes using TOGA (Kirilenko 2023 whole-genome-alignment chain-based projection with intactness classification), CESAR 2.0 (Sharma, Schwede & Hiller 2017 codon-aware exon projection), LiftOff (Shumate & Salzberg 2021 reference-based annotation transfer), Liftover (UCSC), GeMoMa (Keilwagen 2019 evidence-based projection), and Comparative Annotation Toolkit (CAT). Use when transferring annotations from a well-annotated reference to query genome(s), classifying gene-loss vs gene-intact across many genomes at scale, building Zoonomia-style comparative annotations across hundreds of mammals or birds (Kirilenko 2023), detecting pseudogenization, projecting alternative isoforms, or selecting between WGA-anchored (TOGA) vs ortholog-based (LiftOff) annotation transfer strategies.

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Infer integer allele-specific copy number, tumor purity, and ploidy from tumor sequencing by jointly modeling read depth (logR) and B-allele frequency (BAF) with ASCAT, Sequenza, FACETS, PURPLE, and PureCN (tumor-only). Covers the purity-ploidy identifiability problem, the diploid-baseline (dipLogR) anchor, major/minor copy number, loss of heterozygosity, sunrise/contour fit diagnostics, and reconciliation of conflicting fits. Use when tumor analysis needs absolute copy number rather than relative log2, when estimating purity and ploidy, calling LOH or copy-neutral LOH, resolving whole-genome doubling, running tumor-only allele-specific calling, or choosing among ASCAT, Sequenza, FACETS, and PureCN.

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Visualize copy number profiles, segments, allele-specific tracks, and cohort patterns from CNVkit, GATK, ASCAT, FACETS, Sequenza, and other callers. Covers genome-wide and per-chromosome log2 scatter plots, B-allele-frequency/minor-allele-fraction tracks, ideograms, cohort heatmaps, circos views, and caller-native plots. Use when creating publication CNV figures, choosing which plot answers a given question, diagnosing a wrong diploid baseline visually, displaying loss of heterozygosity, or deciding what depth-only plots cannot reveal.

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Classify constitutional (germline) copy number variants for clinical reporting using the 2019 ACMG/ClinGen technical standards points-based framework, with ClassifyCNV and AnnotSV for semi-automated scoring. Covers the separate copy-number-loss and copy-number-gain rubrics, the five-tier classification, ClinGen haploinsufficiency/triplosensitivity and dosage-sensitive regions, de novo and segregation evidence, and population-frequency benign evidence. Use when assigning pathogenic/likely-pathogenic/VUS/likely-benign/benign to a constitutional CNV, scoring a CNV against ACMG/ClinGen criteria, or distinguishing the automatable evidence from the case-specific evidence requiring manual input.

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Quantify homologous recombination deficiency (HRD) from tumor copy number using the three genomic-scar metrics — loss of heterozygosity (LOH), large-scale state transitions (LST), and telomeric allelic imbalance (TAI) — with scarHRD, and via the whole-genome HRDetect and CHORD models. Covers the genomic instability score, the PARP-inhibitor clinical context, whole-genome-doubling correction, and the scar-versus-state distinction. Use when computing an HRD score for PARP-inhibitor eligibility, deriving LOH/LST/TAI scars from allele-specific copy number, deciding between scar-based and mutational-signature HRD methods, or interpreting an HRD result in a BRCA-reverted or low-purity tumor.

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Analyzes differential transcript usage (DTU) and isoform switches with functional consequence prediction (NMD via 50nt rule, ORF disruption, protein domain loss/gain, signal peptide changes, IDR alterations, coding-potential shifts). Tools include IsoformSwitchAnalyzeR v2 (auto-selects satuRn for >5 reps else DEXSeq), the manual DRIMSeq -> DEXSeq/satuRn -> stageR DTU pipeline, and fishpond/swish for inferential-uncertainty-aware DTE. Distinguishes DTU from DGE and DTE; integrates external annotators (CPC2, Pfam, SignalP, IUPred2A or DeepTMHMM). Use when investigating how splicing differences alter protein function or trigger NMD-mediated degradation.

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Use when the user mentions file storage issues, data loss, backup bloat, or asks to audit storage usage.

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Model, simulate, and optimize Serializer/Deserializer (SerDes) systems — serial and parallel links — using MATLAB SerDes Toolbox. Design NRZ and PAM-N links (PAM3 through PAM16) — explore equalization architectures (FFE, CTLE, DFE), sweep or optimize parameters with genetic algorithms, and characterize channels from loss models, S-parameter files, or crosstalk scenarios. Process captured waveforms through equalization chains, build eye diagrams, and decompose jitter. Deliver IBIS-AMI models for Tx, Rx, Redriver, or Retimer by exporting to Simulink and compiling .ami/.ibs/.dll/.so files. Covers the full arc from initial design exploration and parameter optimization to compliance testing and compiled model validation, including custom datapath blocks for nonstandard equalization.

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Dielectric substrates, metal conductors, multi-layer stackups, and loss models (FR4, Rogers, Teflon) for RF PCB simulation. TRIGGER: user asks to set up a substrate, define dielectric properties, create a stackup, select a PCB material (FR4, Rogers, Teflon, etc.), or configure metal conductors. Invoke BEFORE writing dielectric() or metal() code — the API for named vs custom materials differs significantly. SKIP: PCB layout assembly (use matlab-assemble-pcb-layout), transmission line design (use matlab-design-pcb-transmission-line), EM analysis (use matlab-analyze-em), importing a PCB file (use matlab-read-pcb-layout).

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Generate C/C++ or CUDA code from an AI model (PyTorch, LiteRT) using MATLAB Coder or GPU Coder. Use when the user wants to integrate an AI model into an application with code generation as the end goal — generating MEX, CUDA MEX, static library, dynamic library, or executable — or using the model in Simulink for simulation and code generation. Covers PyTorch ExportedProgram (.pt2) via loadPyTorchExportedProgram and LiteRT (.tflite) via loadLiteRTModel (R2026a+). Keywords: PyTorch, torch, .pt2, ExportedProgram, loadPyTorchExportedProgram, invoke, codegen, MEX, CUDA, GPU, C, C++, deploy, AI model, deep learning model, LiteRT, TFLite, TensorFlow Lite, Simulink, slbuild, PyTorch ExportedProgram block, MATLAB Function block, dlosslib, loadLiteRTModel.

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Plan, audit, implement, migrate, or validate localization for multilingual products and websites, including locale scope, market readiness, URL architecture, content coverage, hreflang coordination, rollout, and production verification. Use translation for the actual translation, glossary, and language review work.

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。