「compute」の検索結果

Pull pre-computed ortholog calls from public databases (OrthoDB, Ensembl Compara, OMA browser, eggNOG, PANTHER, KEGG Orthology, HomoloGene) via their REST APIs. Use when orthologs are already curated upstream, when the question is "what is the X ortholog of Y" rather than "how to infer orthology de novo", when batch-mapping gene IDs across species, or when comparing the resources for consensus calls. Encodes confidence-level semantics, 1:1 vs 1:many vs many:many, HomoloGene deprecation, and when to defect to de novo computation.

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Compute genome-to-genome distances (ANI, AAI, dDDH, k-mer Mash) and assign taxonomic classifications using skani (Shaw 2023), FastANI (Jain 2018), pyani / pyANI ANIb / ANIm, OrthoANI (Lee 2016), AAI (amino-acid identity), dDDH via TYGS / GGDC, GTDB-Tk (Chaumeil 2020 standard prokaryote taxonomy), and Mash MinHash (Ondov 2016). Use when delineating prokaryote species (95% ANI threshold; Jain 2018 Nat Commun 9:5114), assigning genomes to GTDB taxonomy with ANI radius, computing genome similarity matrices for clustering, classifying archaea, evaluating MAG (metagenome-assembled genome) species assignment, applying skani for fast metagenomic ANI screening, or reconciling 16S rRNA-based taxonomy with whole-genome ANI.

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Computes and interprets treatment effect measures (OR, RR, RD, HR, NNT) with calibrated confidence intervals (Wilson, Newcombe, Miettinen-Nurminen, MOVER, profile likelihood, Bender NNT) and reports marginal vs conditional estimands per FDA 2023 covariate adjustment guidance. Use when reporting treatment effects in confirmatory trials, comparing effect sizes across studies, or constructing forest plots.

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Computes sample size and power for clinical trials including continuous, binary, and time-to-event endpoints; superiority, non-inferiority, and equivalence designs; FDA 2016 non-inferiority margin selection with M1/M2 framework; Schoenfeld 1981 and Lakatos 1988 for survival; Schuirmann TOST and 80-125% bioequivalence; minimum clinically important difference (MCID) vs δ distinction. Use when justifying trial size in protocol or SAP per CONSORT 2025 item 16a.

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Visualizes ChIP-seq data using deepTools (computeMatrix, plotHeatmap, plotProfile, bamCoverage, bamCompare), pyGenomeTracks (modern INI-driven track plots), Gviz (R browser-style), EnrichedHeatmap (ComplexHeatmap-based), ChIPseeker tag heatmaps, and IGV batch screenshots. Handles bigWig normalization choices (CPM, BPM, RPGC, spike-in scaled), bamCompare operations (log2 ratio, subtract) with SES scaling, k-means clustering of heatmaps for biological subgrouping, and spike-in-scaled tracks for global-shift experiments. Use when generating publication-quality ChIP-seq signal heatmaps, profile plots, genome-browser tracks, or comparing samples visually.

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Assesses ChIP-seq quality across antibody specificity, fragmentation, enrichment, replicate concordance, and library complexity. Computes FRiP, NSC/RSC (phantompeakqualtools), library complexity (NRF/PBC1/PBC2), deepTools plotFingerprint (JS distance, AUC, synthetic JS), ChIPQC, IDR with ENCODE Nself/Nt rules, and detects hyper-ChIPable artifacts. Use when validating an antibody, diagnosing failed peak calls, deciding whether to proceed with downstream analysis, grading against ENCODE thresholds, or auditing replicate concordance.

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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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Check that the UI you actually rendered uses the design system, by reading computed styles in the running app against the project's design tokens. Catches hardcoded hex colors, off-palette backgrounds, invisible or unusable controls, and animations that never ran. Use after building or restyling a component, when a design review is wanted, when a UI looks slightly off but nobody can say why, or when a design system exists and nothing checks whether the code follows it.

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Use when implementing ANY computer vision feature — image analysis, pose detection, person segmentation, subject lifting, text recognition, barcode scanning.

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Implement computer vision features including text recognition (OCR), face detection, barcode scanning, image segmentation, object tracking, and document scanning in iOS apps. Covers both the modern Swift-native Vision API (iOS 18+) and legacy VNRequest patterns, VisionKit DataScannerViewController for live camera scanning, and CoreMLRequest/VNCoreMLRequest for custom model inference. Use when adding OCR, barcode scanning, face detection, or custom Core ML model inference with Vision.

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Extract features from 1D signals using signalTimeFeatureExtractor, signalFrequencyFeatureExtractor, and signalTimeFrequencyFeatureExtractor. Use when computing time-domain features (amplitude, energy, shape factors), frequency-domain features (spectral location, power, bandwidth, PSD), or time-frequency features (spectral shape, instantaneous, ridges, wavelet, EMD-derived) on a per-frame basis. Use when the user asks to "extract features", "compute spectral features", "build a feature table for a classifier", "get per-frame statistics", "run feature extraction on this signal", or describes a vibration / biosignal / radar / sensor signal needing features for downstream ML or analysis. Includes optional GPU acceleration via canUseGPU and gpuArray. Does not cover filter design, audio-specific feature extraction (use audioFeatureExtractor in Audio Toolbox instead), batch dataset orchestration, or 2D / image features.

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Microstrip, stripline, CPW, differential pairs, and crosstalk analysis for impedance-controlled PCB interconnects. TRIGGER: user asks to design or analyze a transmission line (microstrip, stripline, CPW, coplanar, differential pair), extract RLGC or per-unit-length parameters, compute trace impedance, analyze a PCB trace cross-section, or perform crosstalk/coupling analysis. Invoke BEFORE writing code — preferred over RF Toolbox analytical functions (txlineMicrostrip, txlineStripline, txlineCPW). SKIP: EM simulation/S-parameter extraction of an existing component (use matlab-analyze-em), material/stackup definition only (use matlab-manage-pcb-material), building custom non-catalog geometry (use matlab-assemble-pcb-layout), optimization sweeps (use matlab-optimize-pcb-design).

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Integrate antennas into RF systems using MATLAB Antenna Toolbox and RF Toolbox. Covers impedance matching network design (L/Pi/Tee topologies, evaluation parameters, Richards transformation), measured antenna creation (E-field, directivity-only, EmbeddedE, ffsReader import), RF propagation and site planning (txsite/rxsite, coverage, SINR, ray tracing, link budget), and SAR estimation (birdcage+Phantom, conformalArray+Custom3D, direct EHfields). Use when the user wants to match an antenna, create a measuredAntenna, compute coverage or signal strength, perform ray tracing, or estimate SAR.

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Design and analyze electrically large antenna structures using MATLAB Antenna Toolbox. Covers reflector antennas (parabolic, Cassegrain, Gregorian, offset, corner, cylindrical, spherical, custom STL), reflectarrays and reconfigurable intelligent surfaces (RIS), antennas installed on platforms (vehicles, aircraft, ships, satellites), and radar cross section (RCS) analysis. Includes solver selection (MoM-PO, PO, MoM, FMM), mesh control, and GPU acceleration. Use when the user wants to design a dish/reflector antenna, reflectarray, analyze an antenna on a platform, or compute RCS.

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Discover MATLAB Parallel Computing Toolbox clusters on the network and in the cloud, and manage their profiles — list, inspect, import, export, set default, validate, and delete. Use whenever the user asks what parallel computing resources, clusters, or cluster profiles they have or can use — e.g. "what parallel resources do I have", "show my cluster profiles", "list clusters", "what clusters can I run on", "where can I submit jobs" — and for any work with parcluster, parallel.listProfiles, parallel.defaultProfile, MJS / Generic / HPC Server / MJSComputeCloud clusters, .mlsettings files, or profile validation. Does NOT cover job submission, parpool, or parfor.

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S-parameters, insertion loss, fields, currents, mesh control, and solver selection for RF PCB performance validation. TRIGGER: user asks to compute S-parameters, analyze insertion/return loss, extract fields or currents, compare MoM vs FEM, or control mesh for any RF PCB component. Invoke BEFORE writing sparameters() or solver code — API is non-obvious. SKIP: designing or creating components (use the specific matlab-design-pcb-* skill), material/stackup setup only (use matlab-manage-pcb-material), optimization sweeps (use matlab-optimize-pcb-design), PDN/IR-drop analysis (use matlab-analyze-pcb-pdn).

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Use when writing MATLAB functions with arguments blocks — repeating arguments (arguments (Repeating)), .?ClassName property import in constructors, name-value forwarding with namedargs2cell, or migrating from inputParser or validateattributes. Also when reviewing signatures for implicit-conversion pitfalls (size reshaping, class coercion, computed defaults), or when restricting, constraining, or validating function inputs — scalar vs vector enforcement, type rejection, size checking. Also when asked to harden inputs, make a function more robust, tighten input checking, or rewrite for safer input acceptance — even without "validation" or "arguments block" wording. Triggers on: arguments block, mustBe validators, name-value arguments, varargin, inputParser, nargin/narginchk, restrict input, type checking, scalar constraint, harden inputs, defensive programming. Not for: App Designer callbacks, Simulink mask parameters, class inheritance, or runtime validation outside function or property declarations.

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Price financial instruments in MATLAB using the Financial Instruments Toolbox. Route to the appropriate numerical method reference based on the user's request: Monte Carlo simulation (AssetMonteCarlo, IRMonteCarlo, RoughVolMonteCarlo), FFT / Numerical Integration (Vanilla European options), or Interest-Rate Trees (option-embedded bonds with IRTree). Use when the user asks to price financial instruments or compute Greeks using any of these methods. Use one of the following models depending on the pricing method and instrument: Black-Scholes, Bachelier, Heston, Bates, Merton, Hull-White, Black-Karasinski, Black-Derman-Toy, Cox-Ingersoll-Ross, Linear Gaussian 2 Factor (G2PP), Brace-Gatarek-Musiela (BGM), SABR-BGM, RoughBergomi, RoughHeston.

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Patterns for using blockedImage to process large images, harness parallel compute for image processing, and write custom adapters. Use when writing code that creates, processes, or visualizes blockedImage objects, when implementing images.blocked.Adapter subclasses, or when a user needs help with large image data. Always use this skill when working with TIFF,GeoTIFF, .svs, .ndpi, .czi or other WSI, satellite imagery or microscopy volume image formats.

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Import recorded driving sensor data (GPS, camera, lidar, actor tracks, lanes) into scenariobuilder.* objects (GPSData, CameraData, LidarData, ActorTrackData, Trajectory, laneData) and run preprocessing — synchronize, offset correction, crop, normalizeTimestamps, convertTimestamps. Also: compute actor tracks from lidar when no annotations exist, attach camera/lidar mounting + intrinsics, export to MAT/workspace/timetable/script. Use for raw driving dataset files (KITTI, nuScenes, Waymo, Pandaset, ROS/ROS2 bags, .mat, .csv, .mp4) or driving/vehicle/sensor logs that need wrapping. drivingLogAnalyzer (DLA) is OPT-IN ONLY — invoke only on explicit user request ('DLA', 'open in DLA', 'inspect/explore/analyze the recording') or reported sensor problem (sync drift, timestamp mismatch, overlay misalignment). NEVER auto-launch DLA after wrapping (Rule 0). For 'build scenario / export to RoadRunner / drivingScenario / OpenSCENARIO / Unreal / simulate', hand off to matlab-use-scenario-builder.

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Creates MATLAB interfaces to Python image processing and computer vision models from GitHub repositories or pip-installable packages using MPyReq. Use when asked to interface MATLAB with a Python CV/image model (segmentation, depth estimation, object detection, image generation, super-resolution, etc.), given a GitHub repo URL for an image/vision model, or asked to create an MPyReq demo for a deep-learning vision pipeline. Do NOT use for general-purpose Python-MATLAB interfacing, non-vision models (NLP, tabular, audio), model deployment/serving, or MATLAB-only image processing workflows.

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Fit SimBiology model parameters to data — fitproblem, population NLME, virtual patients, and NCA. Use when asked to fit, estimate, calibrate, or compute PK metrics.

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Display images and annotations for image processing, computer vision, and visual inspection. Use when displaying images with imageshow, creating image viewers with viewer2d, adding Regions of Interest (ROI) or annotations, overlaying masks or segmentations, streaming video frames, or building apps with image display.

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AWS Lambda serverless functions for event-driven compute. Use when creating functions, configuring triggers, debugging invocations, optimizing cold starts, setting up event source mappings, or managing layers.

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