Results for “training data”

Authors reproducible bioinformatics pipelines with Snakemake - rules wired by output-file pattern, wildcards and expand() for sample fan-out, checkpoints for runtime-unknown outputs, resource/retry escalation, and conda/container software deployment on HPC and cloud. Use when deciding rule-based (Snakemake) vs channel/dataflow (Nextflow) authoring; wiring rules by OUTPUT-file pattern rather than imperative order; using wildcards + expand() for sample fan-out and constraining them to stop silent mis-routing; adding checkpoints when the set of outputs is unknown until a step runs (dynamic DAG); diagnosing why a job reran (or did not) under the mtime-plus-provenance trigger set; escalating memory on retry for OOM-killed jobs; and porting a Snakemake 7 `--cluster`/remote-provider command to the Snakemake 8+ executor-plugin and storage-plugin model (snakemake-executor-plugin-slurm) with `--software-deployment-method`.

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Standardizes molecular structures using ChEMBL chembl_structure_pipeline and RDKit rdMolStandardize covering sanitization, salt/solvent stripping, neutralization, tautomer canonicalization, stereochemistry standardization, mixture handling, and isotope normalization. Explicitly compares ChEMBL pipeline, canSARchem, and PubChem standardization choices. Use when preparing libraries for QSAR training, joining datasets across sources, deduplicating compound collections, or building canonical compound registries.

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Plan AI fine-tuning projects with data preparation, training, and evaluation. TRIGGERS - Use when user needs help with ai-fine-tuning-plan related tasks.

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Build text and data classification systems with training and evaluation. TRIGGERS - Use when user needs help with ai-classification-system related tasks.

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The live fieldwork layer for psycho-logic — go look at the actual target market NOW instead of reasoning from your training-data stereotype of it. Use when a psycho-logic move needs grounding in a specific place: the user asks 'what do competitors in [region/country] actually do', 'what's the real price band / norm here', 'how do local leaders position themselves', 'research this market before we localise', 'what signals trust to buyers in X', or is about to launch/adapt in a market you haven't studied. Runs structured web research in the local language — local competitors and their signals, price bands, category conventions, review/trust sources, local terminology, taboos and regulations — and synthesises a compact perception profile the four moves consume. Inspired by Rory Sutherland's *Alchemy*. Routed to from psycho-logic; pair with cultural-context (the lens that tells you what to look for). 日本語・中文の相談（「現地の実態を調べて」「调研当地市场」）にも使う。

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Interactive cell annotation and image QC for IMC/MIBI using napari, napari-imc, Mantis Viewer, and cytomapper, covering the pixels-to-cell-table bridge, overlaying masks to catch segmentation/spillover artifacts, inter-annotator variability as the accuracy ceiling, contrast-as-threshold, and building class-balanced ground-truth label sets. Use when manually labeling cells, generating training data for a classifier, QC-ing segmentation on the image, confirming clusters are spatially real, or choosing an annotation viewer.

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Predict peptide-MHC class II (HLA-DR/DQ/DP) binding and presentation for CD4 T-cell epitopes with NetMHCIIpan-4.3 and MixMHC2pred-2.0. Covers why class II is far less reliable than class I (open binding groove, 9-mer register ambiguity, sparse noisy training data, DR>DP>DQ accuracy asymmetry), the DQ/DP heterodimer alpha/beta pairing trap, and the looser 1%/5% %Rank thresholds. Use when predicting CD4 epitopes for vaccine help, mapping class II neoantigens, or scoring long peptides against DR/DQ/DP. For CD8/class I see mhc-binding-prediction.

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Standardizes molecular structures using ChEMBL chembl_structure_pipeline and RDKit rdMolStandardize covering sanitization, salt/solvent stripping, neutralization, tautomer canonicalization, stereochemistry standardization, mixture handling, and isotope normalization. Explicitly compares ChEMBL pipeline, canSARchem, and PubChem standardization choices. Use when preparing libraries for QSAR training, joining datasets across sources, deduplicating compound collections, or building canonical compound registries.

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Expert guidance for Fully Sharded Data Parallel training with PyTorch FSDP - parameter sharding, mixed precision, CPU offloading, FSDP2

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Security checks for repository ingestion — scans repos for poisoned examples, dependency and supply-chain attacks, file/path traversal, format-based attacks, and enforces quarantine-before-commit. Load as part of the secure-* skill sequence whenever an agent reads, ingests, or learns from a GitHub repository. Also load when the user asks to check a repo for poisoned code, scan dependencies, verify supply chain safety, check for path traversal, scan repo files for attacks, or audit a repo before ingestion. Covers Issues 3, 4, 7, 8 from the agent security threat model: poisoned training data, dependency attacks, file/path attacks, and format-based attacks.

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Predict peptide-MHC class II (HLA-DR/DQ/DP) binding and presentation for CD4 T-cell epitopes with NetMHCIIpan-4.3 and MixMHC2pred-2.0. Covers why class II is far less reliable than class I (open binding groove, 9-mer register ambiguity, sparse noisy training data, DR>DP>DQ accuracy asymmetry), the DQ/DP heterodimer alpha/beta pairing trap, and the looser 1%/5% %Rank thresholds. Use when predicting CD4 epitopes for vaccine help, mapping class II neoantigens, or scoring long peptides against DR/DQ/DP. For CD8/class I see mhc-binding-prediction.

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Interactive cell annotation and image QC for IMC/MIBI using napari, napari-imc, Mantis Viewer, and cytomapper, covering the pixels-to-cell-table bridge, overlaying masks to catch segmentation/spillover artifacts, inter-annotator variability as the accuracy ceiling, contrast-as-threshold, and building class-balanced ground-truth label sets. Use when manually labeling cells, generating training data for a classifier, QC-ing segmentation on the image, confirming clusters are spatially real, or choosing an annotation viewer.

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Standardizes molecular structures using ChEMBL chembl_structure_pipeline and RDKit rdMolStandardize covering sanitization, salt/solvent stripping, neutralization, tautomer canonicalization, stereochemistry standardization, mixture handling, and isotope normalization. Explicitly compares ChEMBL pipeline, canSARchem, and PubChem standardization choices. Use when preparing libraries for QSAR training, joining datasets across sources, deduplicating compound collections, or building canonical compound registries.

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Configure engine and version. Pins it in CLAUDE.md; WebSearch fills reference docs when the version is beyond LLM training data.

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Fetch up-to-date, version-specific documentation for any major library (Next.js 16, Sanity, LangGraph, React, Tailwind CSS, Vitest, Framer Motion) via the Context7 MCP server. Use when writing code against unfamiliar or recently-changed framework APIs, when training data may be stale, when resolving deprecations or version-specific syntax, or when the repo warns about framework drift (e.g. the nextjs-agent-rules block in portfolio-v1/AGENTS.md). Invokes the resolve-library-id and get-library-docs MCP tools.

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AI/LLM security offensive checklist: prompt injection, jailbreaking, model extraction, training data poisoning, adversarial inputs, LLM-assisted attack automation, and AI system reconnaissance. Use when assessing AI/ML systems, red-teaming LLMs, or researching AI attack vectors.

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