Search Results for "atomic"

The Atomic Agents framework is designed around the concept of atomicity to be an extremely lightweight and modular framework for building Agentic AI pipelines and applications without sacrificing developer experience and maintainability. The framework provides a set of tools and agents that can be combined to create powerful applications. It is built on top of Instructor and leverages the power of Pydantic for data and schema validation and serialization.

...Instead of relying on a static knowledge graph prepared in advance, the system automatically builds relational structures between entities while processing user queries. Documents are first decomposed into atomic semantic events, which are then represented using multidimensional natural language vectors. These vectors allow the system to identify relationships between concepts and construct a graph representation of knowledge at runtime. The architecture also includes a three-stage retrieval pipeline consisting of recall, expansion, and reranking steps to improve search accuracy. ...

Protenix is an open-source, trainable PyTorch reimplementation of AlphaFold 3, developed by ByteDance with the goal of democratizing high-accuracy protein structure prediction for computational biology and drug-discovery research. Protenix provides a complete pipeline for turning protein sequences (with optional MSA / sequence alignment) or structural inputs (e.g. PDB/CIF) into full 3D atomic-level structure predictions. It supports both “full” models and lightweight variants such as “Protenix-Mini,” offering a trade-off between speed/compute cost and predictive accuracy — making structure prediction accessible even in resource-constrained environments. The project also includes support for constraints (e.g., specifying residue- or atom-level contact constraints, or pocket constraints) to guide predictions toward biologically or experimentally relevant conformations, which enhances its utility for tasks like modeling complexes, ligands, or antibody–antigen interactions.

AtomAI is a Pytorch-based package for deep and machine-learning analysis of microscopy data that doesn't require any advanced knowledge of Python or machine learning. The intended audience is domain scientists with a basic understanding of how to use NumPy and Matplotlib. It was developed by Maxim Ziatdinov at Oak Ridge National Lab. The purpose of the AtomAI is to provide an environment that bridges the instrument-specific libraries and general physical analysis by enabling the seamless...

Uranie is a sensitivity and uncertainty analysis plateform based on the ROOT framework (http://root.cern.ch) . It is developed at CEA, the French Atomic Energy Commission (http://www.cea.fr). It provides various tools for: - data analysis - sampling - statistical modeling - optimisation - sensitivity analysis - uncertainty analysis - running code on high performance computers - etc. Thanks to ROOT, it is easily scriptable in CINT (c++ like syntax) and Python. Is is available both for Unix and Windows platforms (a dedicated platform archive is available on request). ...

...This repository will now be geared towards a straight pytorch translation with some improvements on positional encoding. lhatsk has reported training a modified trunk of this repository, using the same setup as trRosetta, with competitive results. The underlying assumption is that the trunk works on the residue level, and then constitutes to atomic level for the structure module, whether it be SE3 Transformers, E(n)-Transformer, or EGNN doing the refinement.