Results for “models”

Model gene-family birth-death dynamics across a species tree using CAFE5 (Mendes et al 2020 Bioinformatics 36:5516 gamma-distributed rate categories), CAFE5-error (annotation-error-aware), Count (Csurös 2010 ancestral state reconstruction), BadiRate (Librado 2012 likelihood + parsimony), DupliPHY-Family, and ALE/AleRax (for per-family DTL; see [[gene-tree-species-tree-reconciliation]]). Test lineage-specific gene-family expansions and contractions, distinguish biological dynamics from annotation artifacts, account for assembly fragmentation, identify functional enrichment in expanded / contracted families. Use when correlating gene-family changes with phenotype evolution, ranking lineages by adaptive gene-family-rate shifts, post-WGD dosage-balance analysis, or building Birth-death models from OrthoFinder presence/absence matrices.

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Reconstruct ancestral states at internal phylogenetic nodes for sequences (PAML codeml, IQ-TREE --ancestral, GRASP, FastML), discrete traits (corHMM hidden-rate Markov, ape::ace, phytools::make.simmap stochastic mapping, BayesTraits), and continuous traits (phytools::fastAnc, geiger Brownian/OU, RPANDA). Use when designing constructs for ancestral protein resurrection, tracing trait evolution along a tree, performing stochastic character mapping, testing models of trait evolution (BM vs OU vs EB), inferring ancestral genome content via Dollo or DTL reconciliation, or quantifying ancestral-state uncertainty for downstream comparative analyses.

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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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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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Call copy number variants with the GATK best-practices workflows — the somatic CNV pipeline (CollectReadCounts, DenoiseReadCounts with tangent normalization, ModelSegments, CallCopyRatioSegments) and the germline GATK-gCNV pipeline (DetermineGermlineContigPloidy, GermlineCNVCaller cohort/case mode, PostprocessGermlineCNVCalls). Covers panel-of-normals construction, AnnotateIntervals/FilterIntervals, allelic-count integration, and QS-based filtering. Use when integrating CNV calling into a GATK variant pipeline, calling rare germline CNVs from an exome cohort, deciding between the somatic and germline GATK workflows, or diagnosing why tangent normalization removed a real event or why gCNV output has low precision.

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Normalize read-depth copy-ratio profiles and segment them into copy-number regions using circular binary segmentation (CBS, DNAcopy), hidden Markov models, HaarSeg, and fused-lasso methods. Covers GC-content, mappability, and replication-timing (wave-artifact) bias correction, panel-of-normals/PCA denoising, diploid-baseline centering, and algorithm selection by sequencing depth and event size. Use when choosing a segmentation algorithm, correcting depth bias, diagnosing oversegmentation or a mis-centered baseline, tuning CBS or HMM parameters, or understanding why a downstream CNV caller produced fragmented or shifted segments.

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Reconcile gene trees against a species tree under probabilistic models of duplication, transfer, and loss (DTL) using ALE (Szöllősi 2013 amalgamated likelihood), GeneRax (Morel 2020 ML reconciliation), AleRax (Morel 2024 co-estimation), Whale.jl (Bayesian DTL+WGD), RANGER-DTL 2 parsimony, NOTUNG, ecceTERA, and Treerecs. Use when inferring ancestral gene-family content, distinguishing duplication from horizontal transfer from differential loss, rooting deep species trees from gene-content signals (STRIDE / Williams 2017 ALE-rooting), counting DTL events per branch, refining noisy gene trees against a species tree, modeling WGD events jointly with DTL, or producing publication-grade gene-family histories for phylogenomic / comparative analyses.

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Discovers de novo motifs and tests known motif enrichment in ChIP-seq, ATAC-seq, or other peak sequences using HOMER, MEME-ChIP (STREME, CentriMo, TOMTOM, FIMO), monaLisa, and AME. Handles background selection (GC-matched, dinucleotide-shuffled, Markov order-2, peak-flanks), motif databases (JASPAR 2024 CORE PWMs, JASPAR 2026 deep-learning collection, HOCOMOCO v12, HOMER built-in), centrally-enriched motif testing, and differential motif analysis. Use when identifying TF binding motifs in peaks, testing for known TF enrichment, scanning for motif instances, comparing motif content between conditions, or interpreting motifs from deep learning models.

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Builds and applies 3D pharmacophore models using RDKit Pharm3D, the apo2ph4 receptor-based workflow (Heider et al 2022/2023 J Chem Inf Model 63:147-158), Pharmer / Pharmit (search), and PharmacoForge (diffusion-based generation, Flynn et al 2025 Front Bioinform), covering ligand-based pharmacophore (from active set alignment) and receptor-based pharmacophore (from binding pocket geometry). Explicit handling of 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 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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Designs Bayesian clinical trials including Phase I dose-finding (BOIN, CRM, EWOC, mTPI-2), meta-analytic-predictive (MAP) priors with robust mixtures for external data borrowing, EXNEX for basket trials, hierarchical models for safety AE (Berry-Berry), Bayesian platform trials (I-SPY 2, GBM AGILE, REMAP-CAP), and posterior probability stopping rules. Covers FDA Bayesian Devices Guidance (2010), FDA Bayesian Methodology in Drugs Draft (January 2026), BOIN Fit-for-Purpose qualification (December 2021), and Project Optimus dose-optimisation. Use when designing dose-finding studies, platform trials, or sensitivity analyses with informative priors.

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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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Use this skill when the user asks how to pay CDL drivers — cents per mile (CPM), percentage of revenue, hourly, salary, sleeper-team rate, detention pay, driver-pay laws under FLSA (Fair Labor Standards Act), and how each model affects retention + recruitment. Cite FLSA + state wage laws.

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Apply recognition-primed decision making to agents operating under time pressure, uncertainty, and ambiguous cues. Use for situation assessment, RPD-style action selection, and decision-support design in operational settings. NOT for batch optimization, static planning with full information, or tasks where exhaustive search is cheap and harmless.

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Apply recognition-primed decision making to agents operating under time pressure, uncertainty, and ambiguous cues. Use for situation assessment, RPD-style action selection, and decision-support design in operational settings. NOT for batch optimization, static planning with full information, or tasks where exhaustive search is cheap and harmless.

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Threat-models protocols where authority, scarce resources, bonds, bounties, escrow, reputation, ordering, adjudication, or settlement create strategic incentives. Use to test attack utility, conservation, collusion, Sybil resistance, oracle capture, griefing, custody, liquidity, and residual risk. NOT for choosing payment or bond amounts without evidence, smart-contract code audit, legal or employment classification, DeFi trading, admitting workers, or settling claims.

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Methodology for eliciting expert knowledge about cognitive processes, decisions, and mental models in complex tasks

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Tracks cumulative LLM costs across DAG execution and makes real-time decisions to stay within budget. Downgrades models, skips optional nodes, or stops early when cost exceeds thresholds. Use when managing execution budgets, analyzing cost breakdowns, or optimizing model routing for cost. Activate on "cost budget", "too expensive", "reduce cost", "cost optimization", "model downgrade", "budget exceeded". NOT for LLM model selection logic (use llm-router), pricing comparisons across providers, or billing/invoicing.

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Build, debug, optimize, and deploy ComfyUI workflows for diffusion image, video, and audio generation. Activate on: ComfyUI workflow, ComfyUI custom node, ComfyUI API, ComfyUI Manager, KSampler, FLUX in ComfyUI, Wan 2.2 ComfyUI, Hunyuan video ComfyUI, LTX video ComfyUI, IPAdapter, ControlNet ComfyUI, Kijai wrapper, ComfyDeploy, RunComfy, ComfyUI security, GGUF quantization, TeaCache, Nunchaku, ACE-Step ComfyUI, F5-TTS ComfyUI, subgraphs ComfyUI. NOT for: A1111/Forge/Invoke (different UIs), training pipelines from scratch, non-diffusion ML models, or general image-API integrations (use generative-video-2026 / generative-music-audio / media-gen-deployment).

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Semantic image-text matching with CLIP and alternatives. Use for image search, zero-shot classification, similarity matching. NOT for counting objects, fine-grained classification (celebrities, car models), spatial reasoning, or compositional queries. Activate on "CLIP", "embeddings", "image similarity", "semantic search", "zero-shot classification", "image-text matching".

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Designs and audits native-unit capacity reservation, serial admission, ambiguity holds, stop reserves, effect closure, and control-disjoint settlement handoff for consequential agent attempts. Use when scarce capacity must be conserved across retry, rework, resurrection, or compensation. NOT for scheduling work, choosing models, pricing unlike resources into one scalar, authorizing effects, grading work, paying workers, or asserting runtime containment.

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Expert causal reasoning and mental model construction for diagnosis and prediction in complex domains

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Runs a session's fan-out — splits a large request into tiered, recoverable units, dispatches and reconciles them against the repo. Trigger when work needs many agents or spans many repos or files (rebuild, re-architect, sweep, migrate, 'do all of this'); when subagents would launch with no model or effort set; for the plan table (units, models, tokens, meters) before launch; to resume a unit that died or hit a usage limit; when units would share a repo; or say dispatchwright (plan, dispatch, resume, audit, refresh). Tiers come from its own table (scoutwright flags it stale); pacing, pacewright's; hooks, rigwright's; schedules, agentwright's.

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Hands work to a local model served by LM Studio and verifies what comes back. Trigger to offload, delegate or batch work to a local, offline or on-device model; to queue unattended runs that keep only what passes; to ask which installed model fits a job or whether to switch; to size a task before delegating; when a local model returns nothing, repeats itself or drifts on a long list; when LM Studio shares the GPU with an image tool, or to free its hold; or say lmstudiorunner (audit, size, queue, run, status). Reads models from the live LM Studio API. Cloud model picks and prompt text are promptwright's; a schedule's guardrails agentwright's.

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