「ml」の検索結果

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 Nat Commun 12:1302), 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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Analyzes chemical libraries by scaffold using Bemis-Murcko scaffolds, generic frameworks, cyclic skeletons, matched molecular pair (MMP) analysis via mmpdb, R-group decomposition, Free-Wilson analysis, scaffold hopping, and chemotype-aware ML train/test splits. Use when identifying chemotype clusters in a library, deriving SAR transformation rules, decomposing series into R-groups, performing scaffold-balanced QSAR splits, or planning analog campaigns.

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Calculates molecular fingerprints (ECFP/Morgan, FCFP, MACCS, RDKit, AtomPair, TopologicalTorsion, Avalon, MAP4, MHFP6) and physicochemical descriptors (Lipinski, QED, TPSA, Crippen LogP, 3D shape) with explicit choice tables, bit vs count semantics, and partial-charge model selection. Use when featurizing molecules for similarity, QSAR, virtual screening, or ML, or selecting the correct fingerprint for a chemotype-aware task.

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Applies ACMG/AMP 2015 framework with ClinGen SVI specifications, Tavtigian 2018/2020 Bayesian point system, Abou Tayoun 2018 PVS1 decision tree, Pejaver 2022 and Bergquist 2025 calibrated PP3/BP4 thresholds for REVEL/BayesDel/AlphaMissense, Brnich 2020 PS3/BS3 OddsPath, Walker 2023 SpliceAI splicing framework, and AMP/ASCO/CAP 2017 tumor tiers. Use when classifying germline variants P / LP / VUS / LB / B, applying VCEP-specific CSpec rules, computing Whiffin BS1, or assigning cancer Tier I-IV per Li 2017.

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Validates docked / generated protein-ligand poses using PoseBusters physical-validity tests, strain energy quantification, geometric checks (planarity, vdW overlap, bond/angle distortion), and pose-energy reasonableness. Use when QC-ing docking results, comparing classical vs ML docking outputs, or filtering pose lists before SAR analysis.

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Performs alchemical free-energy calculations including relative binding free energy (RBFE / FEP+) and absolute binding free energy (ABFE) via OpenFE, FEP+, GROMACS, AMBER pmemd, and OpenMM with explicit lambda scheduling, soft-core potentials, MBAR/BAR analysis, cycle-closure validation, and protocol-appropriate enhanced sampling. Compares ML alternatives (Boltz-2 affinity, DeepDock). Use when ranking analogs by binding affinity beyond docking accuracy, performing prospective lead optimization, or validating SAR predictions.

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Designs adaptive clinical trials including group-sequential (O'Brien-Fleming, Pocock, Lan-DeMets spending), sample-size re-estimation (blinded Friede-Kieser, unblinded Cui-Hung-Wang, Mehta-Pocock promising zone), seamless Phase 2/3 with treatment-arm selection, population enrichment, and response-adaptive randomisation. Covers FDA 2019 Final Adaptive Designs Guidance, FDA 2022 Master Protocols, and ICH E20 Step 2b/3 draft (June 2025, NOT final). Use when planning interim analyses, sample-size re-estimation, or master/platform-trial designs.

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Reads, validates, and prepares CDISC SDTM and ADaM clinical trial data for analysis. Covers SDTM domain joins (DM, AE, EX, VS, LB, DS), ADaM architecture (ADSL, BDS, OCCDS, ADTTE) with traceability, treatment-emergent AE conventions, baseline derivation, SUPPQUAL/NSV handling, Define-XML 2.1, and Pinnacle 21 / CORE validation. Use when working with clinical trial datasets in CDISC SDTM/ADaM format, preparing analysis-ready data, or validating for regulatory submission.

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Build a differential-ready consensus peakset from per-replicate ATAC-seq peaks using iterative overlap removal, fixed-width re-centering, and majority-rule overlap. Use when generating a stable peak coordinate system for downstream differential accessibility, ML feature engineering, cross-sample comparison, or fixed-width peak counts; covers Corces 2018 iterative overlap (501 bp), DiffBind summit re-centering, and ENCODE consistency rules.

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Estimates bivariate genetic correlation (rg) between traits from GWAS summary statistics or individual-level genotypes using cross-trait LDSC, HDL, LAVA, rho-HESS, GREML-bivariate, Popcorn, and HDL-L. Use when quantifying shared genetic architecture between two traits, screening MR validity before causal inference, distinguishing global from locus-level rg, estimating trans-ancestry rg, separating partial from full causation via LCV gcp, or producing a STROBE-MR-compliant cross-trait sensitivity battery. Cross-trait LDSC intercept absorbs sample overlap and is NOT a bias; HDL is biased under sample overlap above ~5%. High rg between exposure and outcome motivates CHP-aware MR sensitivity (CAUSE, LHC-MR).

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Creates sashimi-style plots showing RNA-seq read coverage and splice junction counts using ggsashimi (general-purpose, condition-grouped overlays), rmats2sashimiplot (rMATS-output-aware), MAJIQ-VOILA (LSV posteriors interactive HTML), leafviz (leafcutter clusters Shiny), Jutils (tool-agnostic heatmaps and sashimi for rMATS/leafcutter/MntJULiP/MAJIQ output), or pyGenomeTracks (multi-track publication figures). Tool choice depends on the upstream differential-splicing tool's output format and the publication vs interactive use case. Use when visualizing specific splicing events, validating differential splicing calls, or producing publication-quality figures.

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Use when implementing, testing, or evaluating ANY Apple Intelligence, on-device AI, or speech-to-text feature. Covers Foundation Models, @Generable, LanguageModelSession, Tool protocol, eval suites, model-as-judge scoring, SpeechTranscriber, CoreML.

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Design and build a high-converting questionnaire-style onboarding flow for your app, modelled on proven conversion patterns from top subscription apps.

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Use when working with iOS/macOS Keychain Services (SecItem queries, kSecClass, OSStatus errors), biometric authentication (LAContext, Face ID, Touch ID), CryptoKit (AES-GCM, ChaChaPoly, ECDSA, ECDH, HPKE, ML-KEM), Secure Enclave, secure credential storage (OAuth tokens, API keys), certificate pinning (SecTrust, SPKI), keychain sharing across apps/extensions, migrating secrets from UserDefaults or plists, or OWASP MASVS/MASTG mobile compliance on Apple platforms.

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Configures and enforces SwiftLint in Swift projects using build tool plugins, run scripts, and CI. Covers .swiftlint.yml configuration, disabled_rules, opt_in_rules, only_rules, analyzer_rules, baselines, autocorrect, swiftlint:disable suppressions, reporter formats (sarif, json, checkstyle), strict and lenient modes, SwiftLintBuildToolPlugin via SimplyDanny/SwiftLintPlugins, swift package plugin swiftlint, Xcode run script phases, CI integration, multiple configuration files, and rollout strategies for existing codebases. Use when setting up SwiftLint, configuring lint rules, suppressing warnings, creating baselines, choosing between build tool plugin and run script, or integrating SwiftLint into CI.

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Use when planning or restructuring what pages a site has and how they connect: hierarchy, navigation, URL patterns, breadcrumbs, and internal linking. Not for XML sitemaps, which are in seo-audit.

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This skill should be used when creating Ultralytics-branded content of any kind, including PDF, PPTX, Canva, or Google Slides presentations, DOCX documents, marketing or newsletter HTML emails, social media post copy or visuals, website or landing page designs, and dataset or model result visuals. Provides official colors, typography, logo rules, naming rules, and tone of voice from ultralytics.com/brand.

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Use this skill any time a spreadsheet file is the primary input or output. This means any task where the user wants to: open, read, edit, or fix an existing .xlsx, .xlsm, .xltx, .csv, or .tsv file (e.g., adding columns, computing formulas, formatting, charting, cleaning messy data); create a new spreadsheet from scratch or from other data sources; or convert between tabular file formats. Trigger especially when the user references a spreadsheet file by name or path — even casually (like "the xlsx in my downloads") — and wants something done to it or produced from it. Also trigger for cleaning or restructuring messy tabular data files (malformed rows, misplaced headers, junk data) into proper spreadsheets. The deliverable must be a spreadsheet file. Do NOT trigger when the primary deliverable is a Word document, HTML report, standalone Python script, database pipeline, or Google Sheets API integration, even if tabular data is involved.

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Trigger when: (1) User mentions "manimgl" or "ManimGL" or "3b1b manim", (2) Code contains `from manimlib import *`, (3) User runs `manimgl` CLI commands, (4) Working with InteractiveScene, self.frame, self.embed(), ShowCreation(), or ManimGL-specific patterns. Best practices for ManimGL (Grant Sanderson's 3Blue1Brown version) - OpenGL-based animation engine with interactive development. Covers InteractiveScene, Tex with t2c, camera frame control, interactive mode (-se flag), 3D rendering, and checkpoint_paste() workflow. NOT for Manim Community Edition (which uses `manim` imports and `manim` CLI).

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Trigger when: (1) User mentions "manim" or "Manim Community" or "ManimCE", (2) Code contains `from manim import *`, (3) User runs `manim` CLI commands, (4) Working with Scene, MathTex, Create(), or ManimCE-specific classes. Best practices for Manim Community Edition - the community-maintained Python animation engine. Covers Scene structure, animations, LaTeX/MathTex, 3D with ThreeDScene, camera control, styling, and CLI usage. NOT for ManimGL/3b1b version (which uses `manimlib` imports and `manimgl` CLI).

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Use this skill when conditioning, loading, preparing, or labeling signal data for analysis or ML training. Covers: cleaning a single signal (fill gaps, remove drift, deoutlier, denoise, resample/align a time base) BEFORE analysis; building a `signalDatastore` pipeline; creating a `labeledSignalSet` for Signal Labeler; deriving labels (filename, folder, in-file, ROI, time-frequency ROI); stratified train/val/test splits; framing long signals; parallel processing; and shaping datastore output for `trainnet`. Triggers include "clean up this signal", "remove drift / detrend", "fill gaps", "remove spikes / outliers", "denoise", "resample to a uniform rate", "align channels", "labels from filenames", "stratified split", "prepare for Signal Labeler", and function names like `fillgaps`, `fillmissing`, `detrend`, `filloutliers`, `smoothdata`, `resample`, `synchronize`, `signalDatastore`, `labeledSignalSet`, `filenames2labels`, `folders2labels`, `splitlabels`, `framesig`, `framelbl`, `createDatastores`.

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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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Use when importing or exporting vehicle data from/to log files (MDF/MF4/DAT, BLF, ASC/TXT), decoding CAN/CAN FD/LIN messages to signals via DBC, ARXML, or LDF databases, writing timetable data to MDF or BLF files, or calling blfread, blfinfo, blfwrite, mdfRead, mdfWrite, mdfCreate, mdfInfo, canSignalImport, canMessageImport, canMessageTimetable, canFDMessageTimetable, canSignalTimetable, or linMessageTimetable.

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RF Toolbox and RF Blockset in MATLAB -- S-parameter I/O, network conversions (S/Z/Y/ABCD/T/H/G, mixed-mode), cascade/de-embedding, rfbudget analysis, circuit composition, matching networks, amplifier stability, mixer spurs, rational fitting, SI channels, baseband processing, Circuit Envelope simulation. Trigger: sparameters, Touchstone, .s2p, .s4p, rfplot, smithplot, rfparam, rfwrite, zparameters, yparameters, abcdparameters, s2sdd, cascadesparams, deembedsparams, rfbudget, noise figure, OIP3, IIP3, amplifier, modulator, nport, rffilter, attenuator, seriesRLC, shuntRLC, lcladder, txline, circuit, setports, clone, matchingnetwork, stabilityk, stabilitymu, powergain, gammams, gammaml, mixerIMT, OpenIF, rational, rationalfit, stepresp, txlineWRLGC, rf.Amplifier, rf.Mixer, rf.Filter, rf.Sparameter, rfsystem, RF Blockset.

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