Results for “deep-learning”

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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Detects allele-specific transcription factor or histone modification binding from heterozygous-variant ChIP-seq using WASP (reference-bias filter; mandatory upstream), RASQUAL (joint QTL + bias-corrected testing), BaalChIP (Bayesian beta-binomial with copy-number-aware overdispersion), and AlleleSeq (personalized diploid genome). Handles imprinted-locus awareness, X-inactivation artifacts, cancer copy-number imbalance, and integration with downstream caQTL / bQTL mapping. Use when identifying variants with allelic effects on TF binding, fine-mapping causal regulatory variants, validating deep-learning variant predictions, or characterizing cis-acting regulatory effects.

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ANDREJ KARPATHY — SKILL COMPLETA v2.0 workflow skill. Use this skill when the user needs Agente que simula Andrej Karpathy — ex-Director of AI da Tesla, co-fundador da OpenAI, fundador da Eureka Labs, e o maior educador de deep learning do mundo and the operator should preserve the upstream workflow, copied support files, and provenance before merging or handing off.

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ANDREJ KARPATHY — SKILL COMPLETA v2.0 workflow skill. Use this skill when the user needs Agente que simula Andrej Karpathy — ex-Director of AI da Tesla, co-fundador da OpenAI, fundador da Eureka Labs, e o maior educador de deep learning do mundo and the operator should preserve the upstream workflow, copied support files, and provenance before merging or handing off.

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Train and deploy neural networks in distributed E2B sandboxes with Flow Nexus

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Builds end-to-end predictive modeling pipelines on tabular datasets—data exploration, preprocessing, baseline modeling, and mandatory optimization—producing valid saved predictions in the required output format. Use for any supervised machine learning or data modeling task, including classification and regression on tabular data, Kaggle-style competitions or submission-file challenges, training a model to predict a target from features, or requests to fit/tune/evaluate models with scikit-learn, XGBoost, Random Forest, Logistic Regression, and similar non-deep-learning methods. Runs fully automated end-to-end without asking the user for intermediate decisions.

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Use when writing or changing PyTorch code — model, Dataset/DataLoader, training and evaluation loops, determinism, mixed precision, torch.compile, checkpoints with safetensors, Hugging Face models, ONNX export, and tests that run on CPU

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Train and deploy neural networks in distributed E2B sandboxes with Flow Nexus

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After the learner demonstrates understanding of a concept, present near-transfer and far-transfer challenges. Use to test whether learning is portable or task-specific — this is what separates understanding from familiarity.

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Create self-explanation prompts that deepen understanding of worked examples, texts, or diagrams. Use when students read material passively without engaging with underlying principles.

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Use when exploring, continuing, or accepting a deep-learning or computer-science research idea. Converts claims into pilot-first experiment matrices covering diagnostics, failure analysis, authorized execution, evaluation, and paper-story viability.

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Use when planning a source-grounded method overview, architecture, pipeline, system/data-flow, mechanism, or agent-workflow figure for a CS or deep-learning paper. Produces an editable figure brief before image generation or manual redrawing; not for plots, tables, or general prose.

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Deep analysis of knowledge distillation techniques for compressing large models into smaller efficient ones

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Strategic patterns for solving intractable problems through cascading approximation, self-improvement, and heterogeneous evaluation from DeepMind's AlphaGo system

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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.

The English summary is being prepared. Showing the original description.

Detects allele-specific transcription factor or histone modification binding from heterozygous-variant ChIP-seq using WASP (reference-bias filter; mandatory upstream), RASQUAL (joint QTL + bias-corrected testing), BaalChIP (Bayesian beta-binomial with copy-number-aware overdispersion), and AlleleSeq (personalized diploid genome). Handles imprinted-locus awareness, X-inactivation artifacts, cancer copy-number imbalance, and integration with downstream caQTL / bQTL mapping. Use when identifying variants with allelic effects on TF binding, fine-mapping causal regulatory variants, validating deep-learning variant predictions, or characterizing cis-acting regulatory effects.

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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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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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METAINFORMANT rules for directory src/metainformant/ml/deep_learning. Use when editing, adding tests, or reviewing code under this path. Read the linked AGENTS.md first; use uv only, write outputs to output/, real implementations.

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Expert guidance for deep learning, transformers, diffusion models, and LLM development with PyTorch, Transformers, Diffusers, and Gradio.

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Guidelines for deep learning development with PyTorch, Transformers, Diffusers, and Gradio for LLM and diffusion model work.

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PyTorch, TensorFlow, neural networks, CNNs, transformers, and deep learning for production

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Data scientist v3 — ML, deep learning, NLP, CV, experimentation, MLOps

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Agente que simula Andrej Karpathy — ex-Director of AI da Tesla, co-fundador da OpenAI, fundador da Eureka Labs, e o maior educador de deep learning do mundo.

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