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Generates 3D conformer ensembles using RDKit ETKDGv3 with knowledge-enhanced distance geometry, MMFF94/UFF force-field optimization, CREST + GFN2-xTB semi-empirical refinement, and macrocycle-aware torsion preferences. Provides explicit decision rules for single vs ensemble conformer use, RMSD pruning, energy windows, conformer count, and force-field choice. Use when preparing 3D ligands for docking, generating descriptor input for 3D QSAR, or sampling macrocycle/peptide conformational ensembles.

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This package is a implementation of biclustering ensemble method MoSBi (Molecular signature Identification from Biclustering). MoSBi provides standardized interfaces for biclustering results and can combine their results with a multi-algorithm ensemble approach to compute robust ensemble biclusters on molecular omics data. This is done by computing similarity networks of biclusters and filtering for overlaps using a custom error model. After that, the louvain modularity it used to extract biclus

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Generates 3D conformer ensembles using RDKit ETKDGv3 with knowledge-enhanced distance geometry, MMFF94/UFF force-field optimization, CREST + GFN2-xTB semi-empirical refinement, and macrocycle-aware torsion preferences. Provides explicit decision rules for single vs ensemble conformer use, RMSD pruning, energy windows, conformer count, and force-field choice. Use when preparing 3D ligands for docking, generating descriptor input for 3D QSAR, or sampling macrocycle/peptide conformational ensembles.

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Design pattern for converting rule-following, checklist, or rubric skills into a fan-out map-reduce ensemble of parallel rigid sub-agents with corroboration-weighted merge; worker model tier and diversity are knobs matched to inference load and stakes, not fixed values. Apply when creating or refactoring a skill or agent that applies 10+ independent criteria in a single pass. Triggers on: 'review against a checklist', 'fan out', 'map reduce review', 'ensemble', 'split the rules', 'apply rubric', or any large ruleset being applied by one agent in one pass. NOT for tight single-pass transforms or rulesets under 5 criteria.

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Generates 3D conformer ensembles using RDKit ETKDGv3 with knowledge-enhanced distance geometry, MMFF94/UFF force-field optimization, CREST + GFN2-xTB semi-empirical refinement, and macrocycle-aware torsion preferences. Provides explicit decision rules for single vs ensemble conformer use, RMSD pruning, energy windows, conformer count, and force-field choice. Use when preparing 3D ligands for docking, generating descriptor input for 3D QSAR, or sampling macrocycle/peptide conformational ensembles.

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Generates 3D conformer ensembles using RDKit ETKDGv3 with knowledge-enhanced distance geometry, MMFF94/UFF force-field optimization, CREST + GFN2-xTB semi-empirical refinement, and macrocycle-aware torsion preferences. Provides explicit decision rules for single vs ensemble conformer use, RMSD pruning, energy windows, conformer count, and force-field choice. Use when preparing 3D ligands for docking, generating descriptor input for 3D QSAR, or sampling macrocycle/peptide conformational ensembles.

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Generates 3D conformer ensembles using RDKit ETKDGv3 with knowledge-enhanced distance geometry, MMFF94/UFF force-field optimization, CREST + GFN2-xTB semi-empirical refinement, and macrocycle-aware torsion preferences. Provides explicit decision rules for single vs ensemble conformer use, RMSD pruning, energy windows, conformer count, and force-field choice. Use when preparing 3D ligands for docking, generating descriptor input for 3D QSAR, or sampling macrocycle/peptide conformational ensembles.

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Generates 3D conformer ensembles using RDKit ETKDGv3 with knowledge-enhanced distance geometry, MMFF94/UFF force-field optimization, CREST + GFN2-xTB semi-empirical refinement, and macrocycle-aware torsion preferences. Provides explicit decision rules for single vs ensemble conformer use, RMSD pruning, energy windows, conformer count, and force-field choice. Use when preparing 3D ligands for docking, generating descriptor input for 3D QSAR, or sampling macrocycle/peptide conformational ensembles.

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Writing a Succession-style ensemble series (继承之战群像剧写法) — distilled from Jesse Armstrong's complete shooting scripts for all four seasons, 39 episodes (Faber 2023), with his introductions and footnotes, plus Frank Rich's and Lucy Prebble's essays on the writers' room. Covers the invisible-act three-test for scripts with no ACT marks, container episodes built on a ceremony's running order, pressure chambers, one core question per episode, finales with fewer and longer scenes, the absent protagonist at the climax, humiliation passed downward, stage directions carrying subtext and "maybe", reversals turned on one word, writing long, alts, the mega-chart, and engineering an ending once the plot engine loses pressure. Use when the user wants a dynastic family drama, a media-power ensemble, a wedding/funeral/summit set piece, a streaming hour with no act breaks, a finale that redraws alliances, or asks how to "Succession-ize" a script or kill a lead mid-season.

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Instrumentation, arranging, and timbral analysis for ensemble and orchestral writing. Covers instrument families (strings, woodwinds, brass, percussion, keyboards), ranges, transpositions, timbral characteristics, scoring techniques, doubling and voicing, Rimsky-Korsakov's orchestration principles, Ravel's and Messiaen's timbral innovations, jazz big band voicing, popular music arranging, and notation conventions. Use when choosing instruments, scoring for ensembles, analyzing orchestral texture, or arranging music for different forces.

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"Combine multiple forecasting models into ensemble predictions for improved accuracy. Use this skill when the user needs to improve forecast reliability, combine ARIMA/Prophet/ETS outputs, or build a robust forecasting pipeline — even if they say 'combine forecasts', 'model averaging', or 'which forecast should I trust'.".

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Implement 10 advanced AI agent node types for any DSL/runtime system — plan compiler, code interpreter, critique loops, intelligent routing, multi-agent ensemble, persistent memory, external API tools, iterative loops, data transforms, and parallel execution. Use this skill whenever the user wants to add agent capabilities to a workflow engine, build an AI orchestration framework, implement Karpathy-style AI upgrades, add new node types to a DSL runtime, or create autonomous agent pipelines. Also trigger when the user mentions AetherLang, flow engines, node types, agent frameworks, or wants to upgrade their AI system with capabilities like self-programming, reflection, routing, ensemble, memory, or tool use.

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Distributed machine learning, data mining, and iterative HPC with Exasol. Covers end-to-end ML pipelines (DISTRIBUTE BY + SET scripts + BucketFS), per-entity federated training with partial_fit and ctx.reset(), batch inference, map-reduce ensemble training, distributed ensemble and SON algorithm for frequent itemset mining (Apriori, FP-Growth, association rules, market-basket analysis), Lua execute script orchestration for iterative algorithms (k-means, SGD, gradient descent), scikit-learn model training, parallel hyperparameter search, per-entity forecasting, anomaly detection, model lifecycle in BucketFS (pickle/joblib/ONNX versioning), GPU acceleration via CUDA SLCs (PyTorch/TensorFlow/RAPIDS), and ML-specific performance tuning (skew, OOM, multi-pass chunking).

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Repeat candidate searches and comparisons while keeping an append-only decision log. Record evidence, compare results with earlier winners, and check replay, freshness, and approval requirements before moving to live trading or production actions.

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• Comparing candidates through repeated trials
• Keeping an evidence trail for decisions
• Reassessing earlier winners with fresh information

Run molecular property predictions, explore molecular shapes, and estimate how compounds bind to proteins through a cloud Python API. Process compound batches and connect modeling steps without maintaining local high-performance computing infrastructure.

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• Predicting properties across a compound library
• Exploring molecular shapes and tautomeric forms
• Estimating how compounds bind to proteins

Run a quick first review of code changes with six specialist agents working in parallel. They check logic, input and output, shared state, resources, missing behavior, and API completeness, then combine duplicate findings into a report ranked by confidence.

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• Running a quick first review of a patch
• Screening diffs to prioritize further investigation
• Checking for missing cleanup and handlers

Review medium to large code changes using checks selected for the actual patch. Analyze the change and surrounding code, assign focused reviews by function, file, or feature, and combine findings with locations, confidence levels, and supporting evidence.

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• Reviewing patches of roughly 50 to 1,000 lines
• Checking risks specific to a changed feature
• Reviewing changes alongside callers and related implementations

Redistricting analysis in R using the redistverse ecosystem. Use whenever the user is working with redist, redistmetrics, ggredist, geomander, adj, alarmdata, PL94171, censable, easycensus, tinytiger, baf, rict, or redistio. Covers the complete pipeline: Census and spatial data loading, adjacency graph construction, SMC/MCMC simulation, constraints (population balance, county splits, VRA compliance), convergence diagnostics, plan metrics (compactness, partisan fairness, splits), visualization, summary tables, and interactive plan drawing. Invoke whenever the user mentions redistricting, gerrymandering, district plans, simulation ensembles, or any redistverse package by name.

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Build deterministic forecast scripts with Earth2Studio (model, data source, IO, inference). Do NOT use for ensemble, diagnostics, data-only fetch, or install.

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Writing plays and screenplays in the Chekhovian mode (契诃夫戏剧法) — distilled from the complete plays (没有父亲的人/普拉东诺夫, 伊凡诺夫, 林妖→万尼亚舅舅, 海鸥, 三姊妹, 樱桃园, nine one-acts) plus Chekhov's own letters, Stanislavsky's and Nemirovich-Danchenko's rehearsal notes and 焦菊隐/童道明 criticism. Covers the four-act mood-based structure without central climax, off-stage events, "correct answer stated in Act 1 and refused", the announced event that never happens, three-layer endings (hope monologue + nihilist line + household action), no-villain conflict with environment, every character's object and catchphrase, one-way love chains, half-step-off dialogue, philosophy cut by thirst, the shortest words for the deepest pain, stage-direction and sound discipline, and how Chekhov revised The Wood Demon into Uncle Vanya. Use when the user wants an ensemble drama, a "nothing happens" play, subtext-heavy dialogue, a family estate / provincial story, an anti-climactic structure, or asks how to "Chekhov-ize" a script.

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Case studies of television series writing (剧集案例库) from primary texts; Sorkin's six West Wing teleplays (act-page tables, eight act-out types); Chase's five Sopranos scripts (the 35-beat A/B/C/D recipe, what a pilot refuses to explain); Fellowes's annotated Downton Abbey season two (19 storylines, 419 footnotes); Waller-Bridge's Fleabag Scriptures (the six-episode half-hour template); Calvisi's eight minute-by-minute pilot beat sheets (Breaking Bad, Mad Men, Game of Thrones and more); Landau's 47-series structure appendix; Miller's Hannibal and HTGAWM breakdowns; Goldberg & Rabkin's beat sheets; Sakamoto Yuji's We Made a Beautiful Bouquet (a feature) and Noh Hee-kyung's The Most Beautiful Goodbye. Use when you want a worked example of how an episode or pilot is built, need real act lengths, scene counts or storyline grids to imitate, are breaking a multi-thread ensemble episode, designing a bottle episode or a finale, writing a relationship or family drama, or ask 某一集是怎么写的 / 这部剧的结构表.

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Infer gene regulatory networks from bulk or general expression data with mutual-information (ARACNe) and tree-ensemble (GENIE3, GRNBoost2) methods, and infer transcription-factor protein activity from regulons with VIPER and msVIPER. Covers the activity-not-edges paradigm, the undirected-association caveat, the DREAM5 wisdom-of-crowds and method-complementarity result, AUPRC-over-AUROC evaluation, and gold-standard incompleteness. Use when inferring a regulatory network from a bulk expression matrix, finding master regulators, or scoring TF activity from a signature. For single-cell motif-pruned regulons see scenic-regulons; for co-expression modules see coexpression-networks.

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Performs 3D shape-based similarity searching using ROCS (OpenEye), USRCAT (ultra-fast), Open3DAlign (RDKit), ESPSim (electrostatic), and ShaEP with explicit handling of Tanimoto-Combo (shape + color), shape vs ECFP4 complementarity, conformer-ensemble searching, alignment optimization, and scaffold hopping. Use when searching for shape-mimicking compounds with different scaffolds, identifying bioisosteric replacements, prospective scaffold hopping, or expanding hit series beyond 2D similarity.

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Builds QSAR / QSPR models using chemprop D-MPNN, MolFormer, Uni-Mol, ChemBERTa, random forest baselines, and Gaussian processes with explicit handling of OECD 5 principles, applicability domain (kNN, leverage, conformal prediction, Mahalanobis), scaffold-balanced splits, ensemble uncertainty, calibration (Platt, isotonic), feature importance (SHAP, atomic attribution), and prospective validation. Use when building target-specific predictive models from in-house bioassay data, ADMET endpoints, or selectivity profiles.

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