GROMACS Copilot is an agent designed to automate molecular dynamics simulations for proteins in water using GROMACS. It handles system setup, simulation execution, and result analysis automatically, providing outputs such as RMSD, RMSF, Rg, and H-bonds. Users can interact with the agent through prompts and API keys from DeepSeek and OpenAI. The tool aims to simplify the process of running MD simulations, allowing users to focus on other tasks while it handles the technical aspects of the simulations.

CrewAI is a cutting-edge framework designed to orchestrate role-playing autonomous AI agents. By fostering collaborative intelligence, CrewAI empowers agents to work together seamlessly, tackling complex tasks. It enables AI agents to assume roles, share goals, and operate in a cohesive unit, much like a well-oiled crew. Whether you're building a smart assistant platform, an automated customer service ensemble, or a multi-agent research team, CrewAI provides the backbone for sophisticated multi-agent interactions. With features like role-based agent design, autonomous inter-agent delegation, flexible task management, and support for various LLMs, CrewAI offers a dynamic and adaptable solution for both development and production workflows.

Agno is a lightweight library for building multi-modal Agents. It is designed with core principles of simplicity, uncompromising performance, and agnosticism, allowing users to create blazing fast agents with minimal memory footprint. Agno supports any model, any provider, and any modality, making it a versatile container for AGI. Users can build agents with lightning-fast agent creation, model agnostic capabilities, native support for text, image, audio, and video inputs and outputs, memory management, knowledge stores, structured outputs, and real-time monitoring. The library enables users to create autonomous programs that use language models to solve problems, improve responses, and achieve tasks with varying levels of agency and autonomy.

FuseMedML is a Python framework designed to accelerate machine learning-based discovery in the medical field by promoting code reuse. It provides a flexible design concept where data is stored in a nested dictionary, allowing easy handling of multi-modality information. The framework includes components for creating custom models, loss functions, metrics, and data processing operators. Additionally, FuseMedML offers 'batteries included' key components such as fuse.data for data processing, fuse.eval for model evaluation, and fuse.dl for reusable deep learning components. It supports PyTorch and PyTorch Lightning libraries and encourages the creation of domain extensions for specific medical domains.

crewAI is a cutting-edge framework for orchestrating role-playing, autonomous AI agents. By fostering collaborative intelligence, CrewAI empowers agents to work together seamlessly, tackling complex tasks. It provides a flexible and structured approach to AI collaboration, enabling users to define agents with specific roles, goals, and tools, and assign them tasks within a customizable process. crewAI supports integration with various LLMs, including OpenAI, and offers features such as autonomous task delegation, flexible task management, and output parsing. It is open-source and welcomes contributions, with a focus on improving the library based on usage data collected through anonymous telemetry.

LLM-on-Ray is a comprehensive solution for building, customizing, and deploying Large Language Models (LLMs). It simplifies complex processes into manageable steps by leveraging the power of Ray for distributed computing. The tool supports pretraining, finetuning, and serving LLMs across various hardware setups, incorporating industry and Intel optimizations for performance. It offers modular workflows with intuitive configurations, robust fault tolerance, and scalability. Additionally, it provides an Interactive Web UI for enhanced usability, including a chatbot application for testing and refining models.

GuideLLM is a powerful tool for evaluating and optimizing the deployment of large language models (LLMs). By simulating real-world inference workloads, GuideLLM helps users gauge the performance, resource needs, and cost implications of deploying LLMs on various hardware configurations. This approach ensures efficient, scalable, and cost-effective LLM inference serving while maintaining high service quality. Key features include performance evaluation, resource optimization, cost estimation, and scalability testing.

SwiftSage is a tool designed for conducting experiments in the field of machine learning and artificial intelligence. It provides a platform for researchers and developers to implement and test various algorithms and models. The tool is particularly useful for exploring new ideas and conducting experiments in a controlled environment. SwiftSage aims to streamline the process of developing and testing machine learning models, making it easier for users to iterate on their ideas and achieve better results. With its user-friendly interface and powerful features, SwiftSage is a valuable tool for anyone working in the field of AI and ML.

This repository contains a sophisticated deterministic graph-based solution for answering complex questions using a controllable autonomous agent. The solution is designed to ensure that answers are solely based on the provided data, avoiding hallucinations. It involves various steps such as PDF loading, text preprocessing, summarization, database creation, encoding, and utilizing large language models. The algorithm follows a detailed workflow involving planning, retrieval, answering, replanning, content distillation, and performance evaluation. Heuristics and techniques implemented focus on content encoding, anonymizing questions, task breakdown, content distillation, chain of thought answering, verification, and model performance evaluation.

Synthora is a lightweight and extensible framework for LLM-driven Agents and ALM research. It aims to simplify the process of building, testing, and evaluating agents by providing essential components. The framework allows for easy agent assembly with a single config, reducing the effort required for tuning and sharing agents. Although in early development stages with unstable APIs, Synthora welcomes feedback and contributions to enhance its stability and functionality.

draive is an open-source Python library designed to simplify and accelerate the development of LLM-based applications. It offers abstract building blocks for connecting functionalities with large language models, flexible integration with various AI solutions, and a user-friendly framework for building scalable data processing pipelines. The library follows a function-oriented design, allowing users to represent complex programs as simple functions. It also provides tools for measuring and debugging functionalities, ensuring type safety and efficient asynchronous operations for modern Python apps.

Pathway is a Python data processing framework for analytics and AI pipelines over data streams. It's the ideal solution for real-time processing use cases like streaming ETL or RAG pipelines for unstructured data. Pathway comes with an **easy-to-use Python API** , allowing you to seamlessly integrate your favorite Python ML libraries. Pathway code is versatile and robust: **you can use it in both development and production environments, handling both batch and streaming data effectively**. The same code can be used for local development, CI/CD tests, running batch jobs, handling stream replays, and processing data streams. Pathway is powered by a **scalable Rust engine** based on Differential Dataflow and performs incremental computation. Your Pathway code, despite being written in Python, is run by the Rust engine, enabling multithreading, multiprocessing, and distributed computations. All the pipeline is kept in memory and can be easily deployed with **Docker and Kubernetes**. You can install Pathway with pip: `pip install -U pathway` For any questions, you will find the community and team behind the project on Discord.

This is the official repository for 'Alignment Data Synthesis from Scratch by Prompting Aligned LLMs with Nothing'. Magpie is a tool designed to synthesize high-quality instruction data at scale by extracting it directly from an aligned Large Language Models (LLMs). It aims to democratize AI by generating large-scale alignment data and enhancing the transparency of model alignment processes. Magpie has been tested on various model families and can be used to fine-tune models for improved performance on alignment benchmarks such as AlpacaEval, ArenaHard, and WildBench.

HF-LLM.rs is a CLI tool for accessing Large Language Models (LLMs) like Llama 3.1, Mistral, Gemma 2, Cohere and more hosted on Hugging Face. It allows interaction with various models, providing input and receiving responses in a terminal environment. Users can select models, input prompts, receive streaming output, and engage in chat mode. The tool supports a variety of models available on Hugging Face infrastructure, with the list continuously updated. Some models may require a Pro subscription for access.

AI-Driven Research Assistant is an advanced AI-powered system utilizing specialized agents for data analysis, visualization, and report generation. It integrates LangChain, OpenAI's GPT models, and LangGraph for complex research processes. Key features include hypothesis generation, data processing, web search, code generation, and report writing. The system's unique Note Taker agent maintains project state, reducing overhead and improving context retention. System requirements include Python 3.10+ and Jupyter Notebook environment. Installation involves cloning the repository, setting up a Conda virtual environment, installing dependencies, and configuring environment variables. Usage instructions include setting data, running Jupyter Notebook, customizing research tasks, and viewing results. Main components include agents for hypothesis generation, process supervision, visualization, code writing, search, report writing, quality review, and note-taking. Workflow involves hypothesis generation, processing, quality review, and revision. Customization is possible by modifying agent creation and workflow definition. Current issues include OpenAI errors, NoteTaker efficiency, runtime optimization, and refiner improvement. Contributions via pull requests are welcome under the MIT License.

GROMACS Copilot is an agent designed to automate molecular dynamics simulations for proteins in water using GROMACS. It handles system setup, simulation execution, and result analysis automatically, providing outputs such as RMSD, RMSF, Rg, and H-bonds. Users can interact with the agent through prompts and API keys from DeepSeek and OpenAI. The tool aims to simplify the process of running MD simulations, allowing users to focus on other tasks while it handles the technical aspects of the simulations.

AlphaFold3 is an implementation of the Alpha Fold 3 model in PyTorch for accurate structure prediction of biomolecular interactions. It includes modules for genetic diffusion and full model examples for forward pass computations. The tool allows users to generate random pair and single representations, operate on atomic coordinates, and perform structure predictions based on input tensors. The implementation also provides functionalities for training and evaluating the model.

Generative AI models have shown tremendous usefulness in increasing accessibility and automation of a wide range of tasks. This repository contains the `biochatter` Python package, a generic backend library for the connection of biomedical applications to conversational AI. It aims to provide a common framework for deploying, testing, and evaluating diverse models and auxiliary technologies in the biomedical domain. BioChatter is part of the BioCypher ecosystem, connecting natively to BioCypher knowledge graphs.

ADMET-AI is a platform for ADMET prediction using Chemprop-RDKit models trained on ADMET datasets from the Therapeutics Data Commons. It offers command line, Python API, and web server interfaces for making ADMET predictions on new molecules. The platform can be easily installed using pip and supports GPU acceleration. It also provides options for processing TDC data, plotting results, and hosting a web server. ADMET-AI is a machine learning platform for evaluating large-scale chemical libraries.

AI-Drug-Discovery-Design is a repository focused on Artificial Intelligence-assisted Drug Discovery and Design. It explores the use of AI technology to accelerate and optimize the drug development process. The advantages of AI in drug design include speeding up research cycles, improving accuracy through data-driven models, reducing costs by minimizing experimental redundancies, and enabling personalized drug design for specific patients or disease characteristics.

NVIDIA BioNeMo Framework is a collection of programming tools, libraries, and models for computational drug discovery. It accelerates building and adapting biomolecular AI models by providing domain-specific, optimized models and tooling for GPU-based computational resources. The framework offers comprehensive documentation and support for both community and enterprise users.

New AI Drug Discovery is a repository focused on the applications of Large Language Models (LLM) in drug discovery. It provides resources, tools, and examples for leveraging LLM technology in the pharmaceutical industry. The repository aims to showcase the potential of using AI-driven approaches to accelerate the drug discovery process, improve target identification, and optimize molecular design. By exploring the intersection of artificial intelligence and drug development, this repository offers insights into the latest advancements in computational biology and cheminformatics.

GROMACS Copilot is an agent designed to automate molecular dynamics simulations for proteins in water using GROMACS. It handles system setup, simulation execution, and result analysis automatically, providing outputs such as RMSD, RMSF, Rg, and H-bonds. Users can interact with the agent through prompts and API keys from DeepSeek and OpenAI. The tool aims to simplify the process of running MD simulations, allowing users to focus on other tasks while it handles the technical aspects of the simulations.

KG-RAG (Knowledge Graph-based Retrieval Augmented Generation) is a task agnostic framework that combines the explicit knowledge of a Knowledge Graph (KG) with the implicit knowledge of a Large Language Model (LLM). KG-RAG extracts "prompt-aware context" from a KG, which is defined as the minimal context sufficient enough to respond to the user prompt. This framework empowers a general-purpose LLM by incorporating an optimized domain-specific 'prompt-aware context' from a biomedical KG. KG-RAG is specifically designed for running prompts related to Diseases.