'prediction' 검색 결과

Infer or annotate TCR antigen specificity by unsupervised clustering (TCRdist/tcrdist3, GLIPH2, clusTCR, GIANA) and database lookup (VDJdb, IEDB, McPAS-TCR), and rank candidates with supervised predictors (ERGO-II, NetTCR-2.x, pMTnet) under explicit caveats. Encodes the central truth that general TCR-epitope prediction for UNSEEN epitopes essentially does not work (collapses to near-random; IMMREP22, Grazioli 2022) because labeled data is dominated by a few immunodominant epitopes and there is no true negative set — so clustering for discovery is the honest task and de-novo binding needs wet-lab validation. Use when annotating TCR specificity or grouping a repertoire. Epitope/MHC context lives in mhc-binding-prediction.

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Rank and prioritize neoantigen/epitope candidates by likely T-cell response using NeoFox feature annotation, PRIME2.0, BigMHC-IM, the Łuksza/Balachandran fitness model (agretopicity + foreignness), and pVACtools tiering. Encodes the field's hard truths that immunogenicity is the least-solved layer (dedicated scores ~AUROC 0.6-0.7, modest PPV), that scores are valid only for RANKING within one patient (never absolute go/no-go or cross-patient), that DAI has anchor-inflation and WT-denominator traps, and that stacking weak correlated scores into one number is a red flag. Use when ordering a candidate list for a vaccine. Binding lives in mhc-binding-prediction; calling in neoantigen-prediction.

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Predicts protein-coding gene structures (exons, introns, UTRs) in eukaryotic genomes with BRAKER3 (RNA-seq + protein evidence), BRAKER1/BRAKER2, GALBA (protein-only), Funannotate (fungi), GeMoMa (homology projection), or Helixer/Tiberius (deep-learning ab initio). Covers the evidence-first tool decision, mandatory soft-masking, the training-set-quality-dominates principle, OrthoDB clade-partition selection, the one-isoform-per-locus and missing-UTR traps, merge/split errors, and reference bias against orphan genes. Use when annotating a newly assembled eukaryotic genome, choosing a gene-prediction pipeline based on available evidence, or diagnosing a poor annotation.

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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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Designs PROTACs, molecular glues, and bivalent degraders with explicit handling of E3 ligase choice (VHL, CRBN, IAP, MDM2, KEAP1), linker design (length, composition, rigidity), ternary complex prediction (PRosettaC, DeepTernary, AlphaFold3), cooperativity (alpha), DC50 / Dmax characterization, hook effect, and prediction-experiment reconciliation. Use when designing targeted protein degraders, planning linker SAR, predicting ternary complex stability, or building generative degrader workflows.

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Trains and applies base-resolution deep learning models on ChIP-seq / ChIP-nexus / CUT&RUN data. Uses BPNet (Avsec 2021 Nat Genet 53:354; soft motif syntax from ChIP-nexus), chromBPNet (Pampari A et al 2024 bioRxiv; bias-factorized base-resolution profiles), EnFormer (Avsec 2021 Nat Methods 18:1196; 196 kb input, ~100 kb effective receptive field), DeepSEA (Zhou 2015; multi-task CNN), and JASPAR 2026 deep-learning collection (1259 BPNet ChIP models). Performs in silico mutagenesis for variant-effect prediction, DeepLIFT/Grad attribution, and TF-MoDISco motif discovery from attribution scores. Use when predicting variant effects on TF binding, discovering soft motif syntax / cooperativity, integrating ChIP-seq with sequence-only predictions, or applying precomputed JASPAR Deep Learning models to new variants.

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Predicts ADMET properties using ADMETlab 3.0 (119 platform features, including 77 prediction models with modeled-endpoint uncertainty), ADMET-AI, DeepChem MolNet, and chemprop D-MPNN with explicit handling of OECD QSAR principles, applicability domain assessment, calibration, hERG/CYP/AMES endpoints, and PAINS / Lipinski / Ro5 / Veber / BBB druglikeness filters. Use when filtering compounds for drug-likeness, prioritizing leads by predicted safety, or building an in-house ADMET QSAR model.

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Performs ML-based protein-ligand pose prediction and scoring using DiffDock-L (diffusion-based), Boltz-1 / Boltz-2 (foundation model with affinity), Chai-1, AlphaFold3 ligand, EquiBind, TANKBind, NeuralPLexer, and hybrid workflows (DiffDock pose + GNINA rescore + PoseBusters QC). Explicit handling of when ML beats classical docking, when classical beats ML, the PB-invalid pose problem, and rescoring as the standard production hybrid. Use when modern docking is needed: foundation-model ligand-pose prediction, AI rescoring of classical poses, or scaffold-hopping in cross-docking scenarios.

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Predicts whether a DNA variant alters mRNA splicing using sequence-based deep-learning tools — SpliceAI (10kb context dilated CNN, clinical default), Pangolin (multi-tissue), MMSplice (modular per-region CNN with calibrated ΔPSI), SpliceTransformer/TrASPr (tissue-aware transformers), SpliceVault (empirical 300K-RNA lookup of likely mis-splicing outcomes), CADD-Splice (composite score). Applies the ClinGen SVI 2023 framework for ACMG/AMP variant interpretation (PVS1, PP3, BP4 evidence codes), HGVS splicing nomenclature (c.123+1G>A, c.123-3T>G, r.spl?), extended-window scoring for deep-intronic pseudoexons, tissue-specific predictions, branchpoint variant detection (BPHunter, LaBranchoR), and splice-switching ASO design. Use when interpreting splice impact of clinical variants, prioritizing VUS, identifying deep-intronic pathogenic variants, or designing ASOs.

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Integrate Core ML models in iOS apps for on-device machine learning inference. Covers model loading (.mlmodel, .mlpackage, .mlmodelc), predictions with auto-generated classes and MLFeatureProvider, compute unit configuration (CPU, GPU, Neural Engine), MLTensor, VNCoreMLRequest, MLComputePlan, multi-model pipelines, and deployment strategies. Use when loading Core ML models, making predictions, configuring compute units, or profiling model performance.

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Answer prediction questions using market trading data, not opinions. Use when the user asks probability questions about geopolitics, economics, markets, industries, or any topic where real money is being traded on the outcome. Examples: 'What's the probability of WW3?', 'Will there be a recession?', 'Is AI in a bubble?', 'When will the Russia-Ukraine war end?', 'Is it a good time to buy gold?', 'Will SPY drop 5% this month?', 'Is NVDA options premium overpriced?'. The skill reads prices from prediction markets, commodities, equities, options chains, derivatives, yield curves, and currencies, then cross-validates multiple signals to produce a structured probability report.

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Expert multiplayer for desync, rollback, dedicated --headless servers, interest culling, and bandwidth spikes: ENet/WebRTC choice, authority, secure RPCs, client prediction/reconcile, and adaptive sync. Trigger on rubber-banding, cheat-able clients, peer floods, late join, or profiler Network spikes — not only greenfield online games. Keywords: multiplayer, RPC, ENetMultiplayerPeer, MultiplayerSynchronizer, authority, client prediction, rollback, interest management, headless, desync.

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Expert patterns for adding multiplayer to single-player games including client-server architecture, authoritative server design, MultiplayerSynchronizer, lag compensation (client prediction, server reconciliation), input buffering, and anti-cheat measures. Use when retrofitting multiplayer, porting to online play, or designing networked gameplay. Trigger keywords: MultiplayerPeer, ENetMultiplayerPeer, SceneMultiplayer, MultiplayerSynchronizer, rpc, rpc_id, multiplayer_authority, client_prediction, server_reconciliation, lag_compensation, rollback.

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Expert multiplayer for desync, rollback, dedicated --headless servers, interest culling, and bandwidth spikes: ENet/WebRTC choice, authority, secure RPCs, client prediction/reconcile, and adaptive sync. Trigger on rubber-banding, cheat-able clients, peer floods, late join, or profiler Network spikes — not only greenfield online games. Keywords: multiplayer, RPC, ENetMultiplayerPeer, MultiplayerSynchronizer, authority, client prediction, rollback, interest management, headless, desync.

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Expert patterns for adding multiplayer to single-player games including client-server architecture, authoritative server design, MultiplayerSynchronizer, lag compensation (client prediction, server reconciliation), input buffering, and anti-cheat measures. Use when retrofitting multiplayer, porting to online play, or designing networked gameplay. Trigger keywords: MultiplayerPeer, ENetMultiplayerPeer, SceneMultiplayer, MultiplayerSynchronizer, rpc, rpc_id, multiplayer_authority, client_prediction, server_reconciliation, lag_compensation, rollback.

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Comprehensive Polymarket skill covering prediction markets, API, trading, market data, and real-time WebSocket data streaming. Build applications with Polymarket services, monitor live trades, and integrate market predictions.

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Use when building, backtesting, operating, or scaling automated trading on prediction markets (Kalshi or similar) — evidence-gated methodology, live-execution safety rails, and falsification protocols distilled from a real live-money campaign

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Venue- and market-type-agnostic strategy, sizing, and backtesting layer for binary prediction markets (Kalshi, Polymarket, ForecastEx). Covers the durable edge thesis, fee-aware selection, fractional-Kelly sizing, and leak-free validation methodology.

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Build ML models for construction predictions. Train and evaluate custom models for cost, duration, and risk prediction.

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Predict construction project costs using Machine Learning. Use Linear Regression, K-Nearest Neighbors, and Random Forest models on historical project data. Train, evaluate, and deploy cost prediction models.

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Use DGL-LifeSci and dgllife for molecular graph learning, molecule featurization, datasets, property prediction, reaction prediction, binding affinity, model-zoo/pretrained models, and molecular generation workflows.

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Use Chemprop 2.2.3 for molecular property prediction: CLI training, prediction, fingerprints, data validation, Python APIs, reaction/atom-bond tasks, uncertainty, hpopt, and conversion workflows.

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Use ColabFold for protein structure prediction workflows: validate FASTA/CSV/A3M inputs, generate MSAs, plan batch predictions, inspect outputs, and troubleshoot optional AlphaFold, MMseqs2, JAX, GPU, and OpenMM dependencies.

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Route AlphaFold protein structure prediction setup, data preparation, local prediction, model configuration, output interpretation, and relaxation workflows.

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