「inference」の検索結果

Estimates time-scaled phylogenies, molecular clock rates, effective reproduction number R_e (or R_t), and population dynamics from dated pathogen genomes using TreeTime (maximum-likelihood) and BEAST2 (Bayesian; strict / uncorrelated lognormal / ORC clocks; constant / exponential / Bayesian Skyline / Skygrid / BICEPS / Birth-Death-Skyline / sampled-ancestor BDSKY priors; structured coalescent via MASCOT). Covers root-to-tip clock signal QC via TempEst, date-randomisation tests (Ramsden 2009; Duchêne 2015), recombination masking via Gubbins and ClonalFrameML before clock inference for recombining bacteria, BDSKY origin-vs-rootHeight pitfalls, sampling-bias correction (Volz & Frost 2014; preferential-sampling extensions), MASCOT structured coalescent for migration, BICEPS-vs-BSP skyline choice, multi-chain BEAST2 convergence diagnostics, and reconciliation between phylodynamic R_e and case-based R_t. Use when dating outbreak origins, estimating substitution rates, inferring R_e through time, building time-calibrated Nextstrain Augur trees, choosing between strict and relaxed clocks, fitting Birth-Death-Skyline (Stadler 2013) models, diagnosing temporal-signal failure, masking recombination before clock inference for *Streptococcus pneumoniae* / *Neisseria gonorrhoeae* / *Klebsiella* / *E. coli* phylodynamics, running MASCOT for structured-population analyses, or using UShER for pandemic-scale placement.

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Estimates time-scaled phylogenies, molecular clock rates, effective reproduction number R_e (or R_t), and population dynamics from dated pathogen genomes using TreeTime (maximum-likelihood) and BEAST2 (Bayesian; strict / uncorrelated lognormal / ORC clocks; constant / exponential / Bayesian Skyline / Skygrid / BICEPS / Birth-Death-Skyline / sampled-ancestor BDSKY priors; structured coalescent via MASCOT). Covers root-to-tip clock signal QC via TempEst, date-randomisation tests (Ramsden 2009; Duchêne 2015), recombination masking via Gubbins and ClonalFrameML before clock inference for recombining bacteria, BDSKY origin-vs-rootHeight pitfalls, sampling-bias correction (Volz & Frost 2014; preferential-sampling extensions), MASCOT structured coalescent for migration, BICEPS-vs-BSP skyline choice, multi-chain BEAST2 convergence diagnostics, and reconciliation between phylodynamic R_e and case-based R_t. Use when dating outbreak origins, estimating substitution rates, inferring R_e through time, building time-calibrated Nextstrain Augur trees, choosing between strict and relaxed clocks, fitting Birth-Death-Skyline (Stadler 2013) models, diagnosing temporal-signal failure, masking recombination before clock inference for *Streptococcus pneumoniae* / *Neisseria gonorrhoeae* / *Klebsiella* / *E. coli* phylodynamics, running MASCOT for structured-population analyses, or using UShER for pandemic-scale placement.

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Build weighted gene co-expression networks to identify modules of co-regulated genes, relate them to phenotypes, and find hub genes using WGCNA, hdWGCNA, MEGENA, CEMiTool, and Gaussian graphical models. Covers signed-network choice, soft-threshold selection, module preservation, and the marginal-vs-partial-correlation distinction. Use when finding co-expression modules, identifying hub genes, relating gene networks to clinical or experimental traits, or building single-cell co-expression networks. For directed TF-target inference see scenic-regulons and grn-inference; for condition rewiring see differential-networks.

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Infer transcription factor regulons from single-cell RNA-seq with pySCENIC by combining GRNBoost2 co-expression, cisTarget motif-enrichment pruning, and AUCell per-cell activity scoring. Covers the motif-pruning-as-directionality principle, regulon specificity scoring, run-to-run stability, and database/species matching. Use when identifying TF regulons, scoring TF activity per cell, finding master regulators of cell identity, or comparing regulon activity across conditions. For enhancer-driven multiomic GRNs see multiomics-grn; for bulk inference and VIPER protein-activity see grn-inference.

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This skill should be used when the user wants to "stress-test a design", "challenge an idea", "red team a proposal", "get critical feedback on a design", "validate a design", "adversarial architecture review", "risk assessment", "設計を検証して", "反論をもらいたい", "設計を批判的にレビュー", "デビルズアドボケート", "ストレステスト", "弱点を指摘して", "穴を見つけて", "この設計で良いか", "リスク評価", "設計のアーキテクチャレビュー", or mentions structured adversarial review of a proposal or design. NOTE: Use this for validating PROPOSALS and DESIGNS through adversarial debate, NOT for generic code review, PR review, or normal review requests (use /codex:review or /codex:adversarial-review for those). Also NOT for investigating unknown bugs (use /agent-dialectics:strong-inference for that).

This skill should be used when the user wants to "synthesize two competing solutions without averaging", "resolve a design/value disagreement by lifting to a higher frame", "止揚 / アウフヘーベン", "矛盾を止揚", "独立案を統合", "平均化せず統合", "contradiction lift", "sublate competing designs", or has two good-but-divergent answers to the same question and wants a higher-order resolution (a selection mechanism) or an honest aporia — not a compromise. NOTE: Use this when two independent solutions diverge and you want to PRESERVE both truth-moments while lifting to a higher frame. Use devils-advocate to stress-test ONE proposal with an assigned opponent, strong-inference to find an unknown cause, and dialectic-loop to validate a claim against a real corpus.

This skill should be used when the user wants to "test a claim against data", "validate an empirical hypothesis", "refine a model/theory with evidence", "characterize a pattern and verify it", "演繹と帰納で検証", "仮説をデータで検証して更新", "実例と反例で確かめる", "弁証法ループ", "主張を現物で裏取り", "傾向分析を検証して精緻化", or mentions iteratively updating a hypothesis by deriving predictions and testing them against a real corpus. NOTE: Use this for VALIDATING/REFINING an empirical claim or model against real data through a derive→test→update loop. Use strong-inference for debugging an UNKNOWN cause, and devils-advocate for adversarially stress-testing a DESIGN proposal.

Optimizes LLM inference with NVIDIA TensorRT for maximum throughput and lowest latency. Use for production deployment on NVIDIA GPUs (A100/H100), when you need 10-100x faster inference than PyTorch, or for serving models with quantization (FP8/INT4), in-flight batching, and multi-GPU scaling.

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Reserved and on-demand GPU cloud instances for ML training and inference. Use when you need dedicated GPU instances with simple SSH access, persistent filesystems, or high-performance multi-node clusters for large-scale training.

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Principled action selection for autonomous agents using Expected Free Energy (EFE) under the Active Inference framework. Each candidate action is scored as G(n) = w_prag * (-E[p_n] * damping) + w_epist * (-Var[p_n] * novelty(n)), where agent beliefs are maintained as per-node Beta distributions and updated via Bayesian observation. Selection is a softmax over -gamma * G, making exploration an automatic consequence of uncertainty rather than a hardcoded epsilon. Precision weights w_prag and w_epist self-adapt via surprise history, shifting the agent between exploitation and exploration regimes without any manually tuned schedule.

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OpenClawのリリース候補に対するCIを実行・監視し、実際のプロバイダー接続やインストール・更新を検証して、失敗の原因と結果を整理するスキルです。

• OpenClawのリリース候補を検証したいとき
• 失敗したCIジョブの調査と再実行
• プロバイダーの認証と推論利用を確認

最新の公開情報と手元の資料を照合し、事実・推測・提案を分けて調査結果をまとめます。単発の確認、選択肢の比較、人物や企業の調査に合わせて調べ方を選ぶスキルです。

• 手元の資料を最新情報で検証したいとき
• 意思決定のために候補を比較したいとき
• 相談先の人物や企業を調べたいとき

llama.cpp local GGUF inference + HF Hub model discovery.

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Set up Actual Computer (actual.inc) inference in Hermes.

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A contract for what the agent does when a long, messy, stream-of-consciousness ramble arrives (usually voice dictation): act on nothing until the echo brief is approved. The echo audits the entire transfer, mission, locked decisions and constraints, open questions, flips and parked tangents, with the model's inferences and guesses quarantined away from the user's own phrasing, so the user verifies what the model believes, not just what it doubts. Use when the user says "let me think out loud" or wants to ramble a bit before building anything, when a message opens with a speech-to-text preamble like "switching to voice, sorry for typos", when input is a long weakly punctuated stream with restarts and mid-message reversals ("actually no, wait, scrap that idea entirely"), or when the user asks to be interviewed about a fuzzy half-formed idea. Includes an optional capture mode for rambles spread across several messages and an optional targeted interview.

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Use this when setting up claude-mem on Cursor: local or remote worker, local host-login observer or remote cmem.ai inference.

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Submit and monitor batch inference jobs from the CLI. Upload and manage files for batch processing, retrieve results, and integrate batch pipelines with CI/CD workflows.

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Interactive CLI for Uni-Mol molecular property prediction training and inference workflows.

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Command-line interface for Ollama - Local LLM inference and model management via Ollama REST API. Designed for AI agents and power users who need to manage models, generate text, chat, and create embeddings without a GUI.

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Hugging Face Transformers for loading Hub models, running pipeline inference, text generation, and Trainer fine-tuning on NLP, vision, audio, and multimodal tasks. Applies when working with AutoModel, pipelines, tokenizers, generation configs, or TrainingArguments within Transformers.

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Fits and diagnoses Python statistical models including OLS, GLM, discrete and mixed models, ARIMA and SARIMAX. Supports coefficient inference, marginal effects, model comparison and time series forecasting with explicit design and uncertainty checks. Used for econometrics and statistical modeling; for guided test selection with APA reporting, see statistical-analysis.

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Supports local computational pathology research with PathML: slide loading and tiling, preprocessing and QC, h5path storage, multiplex quantification, spatial graphs, and bounded model inference. Use for whole-slide H&E, CODEX, Vectra, Mesmer, HoVer-Net, and HACTNet workflows.

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Builds and analyzes phylogenetic trees using MAFFT multiple sequence alignment, IQ-TREE maximum likelihood with ModelFinder and branch support, and FastTree approximate inference. Uses ETE3 for tree summaries and visualization. Applies to homologous nucleotide or protein sequences, microbial gene trees, protein families, and cautiously interpreted dated phylogenies.

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Modal is a serverless cloud platform for running Python on demand, including on-demand GPUs. Use when deploying or serving AI/ML models, running GPU-accelerated workloads (training, fine-tuning, inference), serving web endpoints, scheduling batch jobs, or scaling Python code to cloud containers with the Modal SDK.

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