Results for “model transfer”

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 and analyzes in vivo CRISPR screens in animal tumor models, organoids, and immune-cell adoptive transfers. Covers bottleneck math (250x cells/sgRNA requires ~25M cells implanted; impossible for most syngeneic models, forcing focused libraries), focused library design (Manguso 2017 Nature 547:413 immune screen; Chen 2015 tumor screens), CRISPR-StAR intrinsic-control screening (Uijttewaal 2025 Nat Biotechnol 43:1848), clonal-dynamics-limited detection, tumor-explant DNA recovery, syngeneic vs xenograft vs PDX considerations, and the relationship to downstream MAGeCK / drugZ analysis. Use when designing in vivo CRISPR screens for tumor / immune / metastasis biology, choosing focused vs genome-wide for animal models, addressing bottleneck-induced clonal collapse, picking the syngeneic / xenograft / PDX model, integrating in vivo with in vitro results, or applying CRISPR-StAR for animal experiments.

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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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Analyze single-cell data with scvi-tools, using deep learning to combine datasets, correct differences between experiments, and transfer cell labels. Model guides and reusable scripts cover RNA, protein, chromatin accessibility, spatial data, and downstream analysis.

• Integrate single-cell RNA datasets and correct batch effects
• Analyze paired RNA and protein or RNA and ATAC measurements
• Transfer cell-type labels from reference data

Compare computing devices for a defined AI model workload using memory capacity, computing speed, data transfer, energy use, and cost. Build a comparison that separates predicted performance from measurements and identifies the constraints that determine the choice.

• Choosing hardware for a specific AI model
• Checking whether a model fits in device memory
• Explaining gaps between advertised and measured performance

Reconcile gene trees against a species tree under probabilistic models of duplication, transfer, and loss (DTL) using ALE (Szöllősi 2013 amalgamated likelihood), GeneRax (Morel 2020 ML reconciliation), AleRax (Morel 2024 co-estimation), Whale.jl (Bayesian DL+WGD), RANGER-DTL 2 parsimony, NOTUNG, ecceTERA, and Treerecs. Use when inferring ancestral gene-family content, distinguishing duplication from horizontal transfer from differential loss, rooting deep species trees from gene-content signals (STRIDE / Williams 2017 ALE-rooting), counting DTL events per branch, refining noisy gene trees against a species tree, modeling WGD events jointly with DTL, or producing publication-grade gene-family histories for phylogenomic / comparative analyses.

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Guides management of cross-border data transfers under Asia-Pacific regulatory frameworks including APEC CBPR, ASEAN Model Contractual Clauses, Japan APPI supplementary rules, South Korea PIPA provisions, and Thailand/Singapore PDPA mechanisms. Keywords: APEC CBPR, ASEAN MCCs, APPI, PIPA, PDPA, APAC transfers.

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Maps query single-cell data to reference atlases using scArches transfer learning with scVI and scANVI models. Transfers cell type labels without retraining on combined data. Use when annotating new single-cell datasets using pre-trained reference models.

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Structures secondary direct transactions with pricing methodology, transfer restriction analysis, and ROFR navigation. Use when modeling secondary purchases, pricing founder/employee shares, or structuring tender offers.

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Add an external probabilistic classifier to a decision path without letting it take the path over. Covers finding the externally-graded rows you are already logging, measuring the confidence separation between the overrides it got right and the ones it got wrong, choosing an operating point your data licenses, failing open at the call site, and proving the whole arrangement offline with no API key. Applies to any service returning a score you can order — TypeSafe AI's System One models (Jev) are the worked example. Most of the method transfers to a local model or a second heuristic, with the parts that do not called out where they arise. Use when a rule-based path is wrong often enough to hurt, when someone proposes replacing a heuristic with a model, when a confidence threshold needs a defensible value, or when an oracle already in production has never been graded.

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Reconcile gene trees against a species tree under probabilistic models of duplication, transfer, and loss (DTL) using ALE (Szöllősi 2013 amalgamated likelihood), GeneRax (Morel 2020 ML reconciliation), AleRax (Morel 2024 co-estimation), Whale.jl (Bayesian DL+WGD), RANGER-DTL 2 parsimony, NOTUNG, ecceTERA, and Treerecs. Use when inferring ancestral gene-family content, distinguishing duplication from horizontal transfer from differential loss, rooting deep species trees from gene-content signals (STRIDE / Williams 2017 ALE-rooting), counting DTL events per branch, refining noisy gene trees against a species tree, modeling WGD events jointly with DTL, or producing publication-grade gene-family histories for phylogenomic / comparative analyses.

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Use this skill when the company is about to buy, renew or switch on an AI product or an AI feature inside an existing product, and asks "assess this AI vendor", "do they train on our data", "AI supplier questionnaire", "review the AI terms", "can we use this model provider with customer data", "who are the subprocessors behind this AI tool" or "AI vendor risk assessment". Sizes the review to the use, reads the terms, data processing agreement and documentation before asking questions, checks training use, retention, model changes, subprocessors, transfers, security and exit, and writes an assessment with a recommendation plus the follow-up questions for the vendor.

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Maps query single-cell data onto reference atlases and transfers cell-type labels using scArches surgery (scVI/scANVI), Symphony, Azimuth, CellTypist, scPoli, popV, and foundation models, with explicit out-of-distribution and label-transfer uncertainty. Use when annotating new single-cell datasets against a pre-trained reference, deciding which mapping method fits, or judging whether transferred labels are trustworthy. For de novo clustering and manual annotation see single-cell/cell-annotation; for batch integration without a reference see single-cell/batch-integration.

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Builds and applies 3D pharmacophore models using RDKit Pharm3D, the apo2ph4 receptor-based workflow (Heider et al 2022/2023 J Chem Inf Model 63:147-158), Pharmer / Pharmit (search), and PharmacoForge (diffusion-based generation, Flynn et al 2025 Front Bioinform), covering ligand-based pharmacophore (from active set alignment) and receptor-based pharmacophore (from binding pocket geometry). Explicit handling of feature types, geometric tolerances, partial matching, and pharmacophore-based virtual screening. Use when identifying scaffold-hopping candidates, building shape-and-feature search queries, or transferring SAR across chemotypes.

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Reconcile gene trees against a species tree under probabilistic models of duplication, transfer, and loss (DTL) using ALE (Szöllősi 2013 amalgamated likelihood), GeneRax (Morel 2020 ML reconciliation), AleRax (Morel 2024 co-estimation), Whale.jl (Bayesian DTL+WGD), RANGER-DTL 2 parsimony, NOTUNG, ecceTERA, and Treerecs. Use when inferring ancestral gene-family content, distinguishing duplication from horizontal transfer from differential loss, rooting deep species trees from gene-content signals (STRIDE / Williams 2017 ALE-rooting), counting DTL events per branch, refining noisy gene trees against a species tree, modeling WGD events jointly with DTL, or producing publication-grade gene-family histories for phylogenomic / comparative analyses.

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

Builds and applies 3D pharmacophore models using RDKit Pharm3D, the apo2ph4 receptor-based workflow (Heider et al 2022/2023 J Chem Inf Model 63:147-158), Pharmer / Pharmit (search), and PharmacoForge (diffusion-based generation, Flynn et al 2025 Front Bioinform), covering ligand-based pharmacophore (from active set alignment) and receptor-based pharmacophore (from binding pocket geometry). Explicit handling of feature types, geometric tolerances, partial matching, and pharmacophore-based virtual screening. Use when identifying scaffold-hopping candidates, building shape-and-feature search queries, or transferring SAR across chemotypes.

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

Reconcile gene trees against a species tree under probabilistic models of duplication, transfer, and loss (DTL) using ALE (Szöllősi 2013 amalgamated likelihood), GeneRax (Morel 2020 ML reconciliation), AleRax (Morel 2024 co-estimation), Whale.jl (Bayesian DTL+WGD), RANGER-DTL 2 parsimony, NOTUNG, ecceTERA, and Treerecs. Use when inferring ancestral gene-family content, distinguishing duplication from horizontal transfer from differential loss, rooting deep species trees from gene-content signals (STRIDE / Williams 2017 ALE-rooting), counting DTL events per branch, refining noisy gene trees against a species tree, modeling WGD events jointly with DTL, or producing publication-grade gene-family histories for phylogenomic / comparative analyses.

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

Builds and applies 3D pharmacophore models using RDKit Pharm3D, the apo2ph4 receptor-based workflow (Heider et al 2022/2023 J Chem Inf Model 63:147-158), Pharmer / Pharmit (search), and PharmacoForge (diffusion-based generation, Flynn et al 2025 Front Bioinform), covering ligand-based pharmacophore (from active set alignment) and receptor-based pharmacophore (from binding pocket geometry). Explicit handling of feature types, geometric tolerances, partial matching, and pharmacophore-based virtual screening. Use when identifying scaffold-hopping candidates, building shape-and-feature search queries, or transferring SAR across chemotypes.

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Inspect Blender characters and animations using bone data, coordinates, and ground contact measurements alongside images. Helps diagnose foot sliding, orientation mismatches, and twisting, with reports that distinguish confirmed problems from likely causes and required fixes.

• Checking foot sliding and floor penetration in a walk cycle
• Comparing character facing direction with travel direction
• Inspecting poses after transferring motion between skeletons

Turn rambling messages or voice dictation into a structured brief covering goals, decisions, open questions, reversals, and parked ideas. Separate the agent’s assumptions from the user’s statements and confirm understanding before work begins.

• Organize ideas captured through voice dictation
• Confirm requirements before starting work
• Collect thoughts across multiple messages

Edit images with AI models hosted on fal.ai. Use the skill to change an image's style, remove its background or unwanted objects, or repaint selected areas through inpainting, which replaces part of an image.

• Change an image's visual style
• Remove an image background
• Remove unwanted objects from an image

Builds and applies 3D pharmacophore models using RDKit Pharm3D, the apo2ph4 receptor-based workflow (Heider et al. 2023), Pharmer / Pharmit for search, and PharmacoForge for protein-pocket-conditioned pharmacophore generation (Flynn et al. 2025), covering ligand-based pharmacophores from active-set alignment and receptor-based pharmacophores from binding-pocket geometry. Explicitly handles feature types, geometric tolerances, partial matching, and pharmacophore-based virtual screening. Use when identifying scaffold-hopping candidates, building shape-and-feature search queries, or transferring SAR across chemotypes.

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Identify a linear dynamic model from input-output or time-series data using MATLAB System Identification Toolbox. Use when estimating transfer function, state-space, ARX, ARMAX, BJ, OE polynomial or process models from measurement data.

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A robust and outlier-aware method for testing differential tissue composition from single-cell data. This model can infer changes in tissue composition and heterogeneity, and can produce realistic data simulations based on any existing dataset. This model can also transfer knowledge from a large set of integrated datasets to increase accuracy further.

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