Results for “gene-prediction”

Integrates multi-dimensional health data to detect anomalies, predict risks (hypertension, diabetes, cardiovascular), and generate personalized recommendations and interactive HTML reports.

Predicts tissue or cell-type gene expression (log TPM and TPM) from a TSS-centered DNA sequence using the hosted Genomic Intelligence G0 Expression model, conditioned on a free-text cell-type description.

Detect promoter regions in DNA sequences by calling the Genomic Intelligence G0 transformer (GENA-LM BERT Large) hosted API. Returns per-window promoter probabilities and called regions as a report and JSON, from a single FASTA input.

Guides usage of the Gemini API on Agent Platform with the Google Gen AI SDK, covering SDK usage (Python, JS/TS, Go, Java, C#), capabilities like multimodal inputs, tools, media generation, caching, batch prediction, and Live API.

Detect splice donor and acceptor sites in DNA sequences using the Genomic Intelligence G0 BigBird transformer, via the hosted /v1/tasks/splice/predict API. Returns per-position site probabilities and called sites.

Predicts enhancer activity in DNA sequences using the hosted Genomic Intelligence G0 DeepSTARR model, returning per-window activity scores.

Simulates meiotic recombination to produce offspring genomes from parent pairs, modeling Mendelian segregation, de novo mutation, sex determination, trait inference, and clinical evaluation against a disease registry.

Model interpretability and explainability using SHAP (SHapley Additive exPlanations). Use this skill when explaining machine learning model predictions, computing feature importance, generating SHAP plots (waterfall, beeswarm, bar, scatter, force, heatmap), debugging models, analyzing model bias or fairness, comparing models, or implementing explainable AI. Works with tree-based models (XGBoost, LightGBM, Random Forest), deep learning (TensorFlow, PyTorch), linear models, and any black-box model.

Train unsupervised machine learning models on genomic interval data from BED files, including region embeddings, single-cell ATAC-seq analysis, and consensus peak building.

Performs differential expression analysis on bulk RNA-seq or pseudo-bulk count matrices with QC, PCA, and contrast testing.

Predicts chromatin state across 919 tracks (histone marks, DNase, TF binding) for DNA sequences via the hosted Genomic Intelligence API, producing a report and JSON results.

Scores genetic compatibility between all male-female pairings in a Genomebook generation, ranking optimal mating pairs based on heterozygosity, trait complementarity, and disease risk.

Predict molecular properties, train graph neural networks, and run drug discovery workflows using DeepChem's featurizers, models, and MoleculeNet benchmarks.

Automates genome-wide association studies from genotype files to publication-ready results, running PLINK2 QC and REGENIE regression with Manhattan and QQ plots.

Infer gene regulatory networks from gene expression data using scalable algorithms (GRNBoost2, GENIE3) with support for distributed computation.

Mathematical AI interpretability with sheaf cohomology, spectral analysis, causal inference, and hallucination prevention

Provides guidance on using the Aeon library for time series forecasting, covering model selection, implementation, and evaluation.

Predict continuous values from temporal sequences using aeon's time series regressors, covering convolutional, deep learning, distance-based, feature-based, hybrid, interval-based, and shapelet-based approaches.

Computes phylogenetic distance matrices and trees from genomic VCF or FASTA data using the fastreeR hybrid Java/Python toolkit.

Model interpretability and explainability using SHAP (SHapley Additive exPlanations). Use this skill when explaining machine learning model predictions, computing feature importance, generating SHAP plots (waterfall, beeswarm, bar, scatter, force, heatmap), debugging models, analyzing model bias or fairness, comparing models, or implementing explainable AI. Works with tree-based models (XGBoost, LightGBM, Random Forest), deep learning (TensorFlow, PyTorch), linear models, and any black-box model.

Model interpretability and explainability using SHAP (SHapley Additive exPlanations). Use this skill when explaining machine learning model predictions, computing feature importance, generating SHAP plots (waterfall, beeswarm, bar, scatter, force, heatmap), debugging models, analyzing model bias or fairness, comparing models, or implementing explainable AI. Works with tree-based models (XGBoost, LightGBM, Random Forest), deep learning (TensorFlow, PyTorch), linear models, and any black-box model.

Model interpretability and explainability using SHAP (SHapley Additive exPlanations). Use this skill when explaining machine learning model predictions, computing feature importance, generating SHAP plots (waterfall, beeswarm, bar, scatter, force, heatmap), debugging models, analyzing model bias or fairness, comparing models, or implementing explainable AI. Works with tree-based models (XGBoost, LightGBM, Random Forest), deep learning (TensorFlow, PyTorch), linear models, and any black-box model.

Use for writing, reviewing, debugging, testing, or diagnosing Python Bayesian models built directly with PyMC, including Model, coords/dims, Data, random variables, potentials, posterior sampling, prior/posterior predictive checks, and InferenceData output. Trigger on model geometry, shape errors, divergences, sampler choice, mutable prediction data, and probabilistic validation. Do not use for Bambi formula models, NumPyro/JAX programs, ArviZ-only analysis of existing draws, deterministic optimization, or general statistics without PyMC code.

Automatically rig 3D models with UniRig (VAST-AI-Research, SIGGRAPH'25) — predict a skeleton, predict skinning weights, and merge the rig back onto the original mesh. Use when the user wants auto-rigging for .obj/.fbx/.glb/.gltf/.dae/.vrm assets, a skeleton or skin weights for a character or creature, a UniRig environment prepared on a CUDA machine, batch rigging of a model directory, or an honest comparison between UniRig, SkinTokens, Tripo, Mixamo, AccuRig, and Blender Rigify. Triggers on: unirig, auto rig, auto-rigging, 3D rigging, skeleton prediction, skinning weights, rig a character, armature generation, rigged glb, rigged fbx, bone weights.

Predict biomolecular complexes with Chai-1, an open AlphaFold3-style model that folds multi-entity assemblies (proteins, ligands, nucleic acids) from a single typed FASTA — strong on antibody–antigen and protein–ligand complexes, with optional MSA and restraint inputs. Use when predicting an antibody–antigen complex, folding a mixed protein/ligand/nucleic-acid assembly described in one FASTA, or generating a complex with experimental restraints. For binding-affinity prediction or a ligand-focused co-fold prefer alterlab-boltz; for protein-only or protein–protein folding prefer alterlab-alphafold; to dock into a fixed receptor prefer alterlab-diffdock. Part of the AlterLab Academic Skills suite.