Results for “molecular-featurization”

Molecular machine learning toolkit. Property prediction (ADMET, toxicity), GNNs (GCN, MPNN), MoleculeNet benchmarks, pretrained models, featurization, for drug discovery ML.

Featurização molecular para ML (100+ featurizadores). ECFP, MACCS, descritores, modelos pré-treinados (ChemBERTa), converter SMILES em features, para QSAR e ML molecular.

Convert chemical structures (SMILES or RDKit molecules) into numerical representations for machine learning, covering 100+ featurizers including ECFP, MACCS, descriptors, and pretrained models like ChemBERTa, with support for QSAR modeling and virtual screening.

Featurizes molecules for machine learning with molfeat (100+ featurizers) — ECFP/MACCS/MAP4 fingerprints, RDKit and Mordred physicochemical descriptors, and pretrained embeddings (ChemBERTa, ChemGPT, GIN) exposed as scikit-learn transformers that convert SMILES into feature vectors. Use when turning molecules into ML-ready feature matrices for QSAR/QSPR or virtual screening, or benchmarking fingerprint against descriptor and embedding representations; for training models and MoleculeNet benchmarks on those features prefer alterlab-deepchem, and for low-level fingerprint or descriptor primitives prefer alterlab-rdkit. Part of the AlterLab Academic Skills suite.

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

Convert chemical structures (SMILES or RDKit molecules) into numerical representations for machine learning using 100+ featurizers, including ECFP, MACCS, descriptors, and pretrained models like ChemBERTa.

Molecular machine learning toolkit. Property prediction (ADMET, toxicity), GNNs (GCN, MPNN), MoleculeNet benchmarks, pretrained models, featurization, for drug discovery ML.

Quantize LLMs to 8-bit or 4-bit for 50-75% memory reduction with minimal accuracy loss using bitsandbytes. Supports INT8, NF4, FP4 formats, QLoRA training, and 8-bit optimizers.

Molecular machine learning toolkit. Property prediction (ADMET, toxicity), GNNs (GCN, MPNN), MoleculeNet benchmarks, pretrained models, featurization, for drug discovery ML.

Diffusion-based molecular docking. Predict protein-ligand binding poses from PDB/SMILES, confidence scores, virtual screening, for structure-based drug design. Not for affinity prediction.

Applies medicinal-chemistry filters with the medchem library — drug-likeness rules (Lipinski, Veber), PAINS filters, structural alerts, and molecular complexity metrics for compound prioritization and library cleanup. Use when filtering or triaging a compound library, flagging PAINS or reactive groups, or assessing drug-likeness of candidate molecules. Part of the AlterLab Academic Skills suite.

GGUF format and llama.cpp quantization for efficient CPU/GPU inference. Use when deploying models on consumer hardware, Apple Silicon, or when needing flexible quantization from 2-8 bit without GPU requirements.

GGUF format and llama.cpp quantization for efficient CPU/GPU inference. Use when deploying models on consumer hardware, Apple Silicon, or when needing flexible quantization from 2-8 bit without GPU requirements.

Diffusion-based molecular docking. Predict protein-ligand binding poses from PDB/SMILES, confidence scores, virtual screening, for structure-based drug design. Not for affinity prediction.

Spectral similarity and compound identification for metabolomics. Use for comparing mass spectra, computing similarity scores (cosine, modified cosine), and identifying unknown compounds from spectral libraries. Best for metabolite identification, spectral matching, library searching. For full LC-MS/MS proteomics pipelines use pyopenms.

Cloud-based quantum chemistry platform with Python API. Preferred for computational chemistry workflows including pKa prediction, geometry optimization, conformer searching, molecular property calculations, protein-ligand docking (AutoDock Vina), and AI protein cofolding (Chai-1, Boltz-1/2). Use when tasks involve quantum chemistry calculations, molecular property prediction, DFT or semiempirical methods, neural network potentials (AIMNet2), protein-ligand binding predictions, or automated computational chemistry pipelines. Provides cloud compute resources with no local setup required.

Diffusion-based molecular docking. Predict protein-ligand binding poses from PDB/SMILES, confidence scores, virtual screening, for structure-based drug design. Not for affinity prediction.

Constraint-based metabolic modeling (COBRA). FBA, FVA, gene knockouts, flux sampling, SBML models, for systems biology and metabolic engineering analysis.

Cardinality and model family jointly determine the encoding.

Nocaps: Novel Object Captioning at Scale

GGUF format and llama.cpp quantization for efficient CPU/GPU inference. Use when deploying models on consumer hardware, Apple Silicon, or when needing flexible quantization from 2-8 bit without GPU requirements.

Access AI-ready drug discovery datasets and benchmarks from Therapeutics Data Commons, covering ADME, toxicity, drug-target interactions, and molecular generation with standardized splits and evaluation metrics.

Process and analyze mass spectrometry data with the Matchms Python library, including importing spectra, filtering peaks, calculating similarity scores, and building reproducible analytical workflows.

Perform coverage-guided fuzzing of compiled binaries using AFL++ to discover memory corruption, crashes, and security vulnerabilities.

Therapeutics Data Commons. AI-ready drug discovery datasets (ADME, toxicity, DTI), benchmarks, scaffold splits, molecular oracles, for therapeutic ML and pharmacological prediction.

Universal transformation λ(ο,K).τ with recursive self-improvement. USE WHEN routing reasoning, validating knowledge graphs, preparing CICM/ANZCA examinations, or when self-improvement of reasoning/architecture/context is required. Routes queries through R0-R3 complexity pipelines, validates topology (η≥target) and governance (KROG), emits per style (Φ), and compounds learnings into knowledge K. Triggers on complexity assessment, multi-step reasoning, examination mode, or /λ invocation.

Essential fuzzing payloads: SQL injection, command injection, special characters. Curated essentials for vulnerability testing.

Medicinal chemistry filters. Apply drug-likeness rules (Lipinski, Veber), PAINS filters, structural alerts, complexity metrics, for compound prioritization and library filtering.

Model, simulate, and optimize Serializer/Deserializer (SerDes) systems — serial and parallel links — using MATLAB SerDes Toolbox. Design NRZ and PAM-N links (PAM3 through PAM16) — explore equalization architectures (FFE, CTLE, DFE), sweep or optimize parameters with genetic algorithms, and characterize channels from loss models, S-parameter files, or crosstalk scenarios. Process captured waveforms through equalization chains, build eye diagrams, and decompose jitter. Deliver IBIS-AMI models for Tx, Rx, Redriver, or Retimer by exporting to Simulink and compiling .ami/.ibs/.dll/.so files. Covers the full arc from initial design exploration and parameter optimization to compliance testing and compiled model validation, including custom datapath blocks for nonstandard equalization.

Detect poisoned training data and backdoored models across the ML pipeline using statistical analysis, activation clustering, and spectral signatures.

Systematically fuzz web applications for hidden content and input validation vulnerabilities across directories, files, parameters, and authentication bypasses.

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.