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.

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.

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.

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.

AI2BMD is a program for efficiently simulating protein molecular dynamics with ab initio accuracy. The repository contains datasets, simulation programs, and public materials related to AI2BMD. It provides a Docker image for easy deployment and a standalone launcher program. Users can run simulations by downloading the launcher script and specifying simulation parameters. The repository also includes ready-to-use protein structures for testing. AI2BMD is designed for x86-64 GNU/Linux systems with recommended hardware specifications. The related research includes model architectures like ViSNet, Geoformer, and fine-grained force metrics for MLFF. Citation information and contact details for the AI2BMD Team are provided.

llm-ls is a Language Server Protocol (LSP) server that utilizes Large Language Models (LLMs) to enhance the development experience. It aims to serve as a foundation for IDE extensions by simplifying interactions with LLMs, enabling lightweight extension code. The server offers features such as context-based prompt generation, telemetry for retraining, code completion based on AST analysis, and compatibility with various backends like Hugging Face's APIs and llama.cpp server bindings.

Anda is an AI agent framework built with Rust, integrating ICP blockchain and TEE support. It aims to create a network of highly composable, autonomous AI agents across industries to advance artificial intelligence. Key features include composability, simplicity, trustworthiness, autonomy, and perpetual memory. Anda's vision is to build a collaborative network of agents leading to a super AGI system, revolutionizing AI technology applications and creating value for society.

HumanLayer is a Python toolkit designed to enable AI agents to interact with humans in tool-based and asynchronous workflows. By incorporating humans-in-the-loop, agentic tools can access more powerful and meaningful tasks. The toolkit provides features like requiring human approval for function calls, human as a tool for contacting humans, omni-channel contact capabilities, granular routing, and support for various LLMs and orchestration frameworks. HumanLayer aims to ensure human oversight of high-stakes function calls, making AI agents more reliable and safe in executing impactful tasks.

EasyDist is an automated parallelization system and infrastructure designed for multiple ecosystems. It offers usability by making parallelizing training or inference code effortless with just a single line of change. It ensures ecological compatibility by serving as a centralized source of truth for SPMD rules at the operator-level for various machine learning frameworks. EasyDist decouples auto-parallel algorithms from specific frameworks and IRs, allowing for the development and benchmarking of different auto-parallel algorithms in a flexible manner. The architecture includes MetaOp, MetaIR, and the ShardCombine Algorithm for SPMD sharding rules without manual annotations.

BitMat is a Python package designed to optimize matrix multiplication operations by utilizing custom kernels written in Triton. It leverages the principles outlined in the "1bit-LLM Era" paper, specifically utilizing packed int8 data to enhance computational efficiency and performance in deep learning and numerical computing tasks.

Nixtla is a production-ready generative pretrained transformer for time series forecasting and anomaly detection. It can accurately predict various domains such as retail, electricity, finance, and IoT with just a few lines of code. TimeGPT introduces a paradigm shift with its standout performance, efficiency, and simplicity, making it accessible even to users with minimal coding experience. The model is based on self-attention and is independently trained on a vast time series dataset to minimize forecasting error. It offers features like zero-shot inference, fine-tuning, API access, adding exogenous variables, multiple series forecasting, custom loss function, cross-validation, prediction intervals, and handling irregular timestamps.

The Codebase Context Specification (CCS) project aims to standardize embedding contextual information within codebases to enhance understanding for both AI and human developers. It introduces a convention similar to `.env` and `.editorconfig` files but focused on documenting code for both AI and humans. By providing structured contextual metadata, collaborative documentation guidelines, and standardized context files, developers can improve code comprehension, collaboration, and development efficiency. The project includes a linter for validating context files and provides guidelines for using the specification with AI assistants. Tooling recommendations suggest creating memory systems, IDE plugins, AI model integrations, and agents for context creation and utilization. Future directions include integration with existing documentation systems, dynamic context generation, and support for explicit context overriding.

Sentience is a tool that allows developers to create autonomous AI agents on-chain with verifiable proofs. It leverages a Trusted Execution Environment (TEE) architecture to ensure secure execution of AI calls and provides transparency through cryptographic attestations posted on Solana's blockchain. The tool enhances market potential by transforming agents into cryptographically verifiable entities, addressing the need for trust in AI development. Sentience offers features like OpenAI compatibility, on-chain verifiability, an explorer for agent history, and an easy-to-use developer experience. The repository includes SDKs for Python and JavaScript, along with components for verified inference and instructions for verifying the TEE architecture.

Craftium is an open-source platform based on the Minetest voxel game engine and the Gymnasium and PettingZoo APIs, designed for creating fast, rich, and diverse single and multi-agent environments. It allows for connecting to Craftium's Python process, executing actions as keyboard and mouse controls, extending the Lua API for creating RL environments and tasks, and supporting client/server synchronization for slow agents. Craftium is fully extensible, extensively documented, modern RL API compatible, fully open source, and eliminates the need for Java. It offers a variety of environments for research and development in reinforcement learning.

CoLLM is a novel method that integrates collaborative information into Large Language Models (LLMs) for recommendation. It converts recommendation data into language prompts, encodes them with both textual and collaborative information, and uses a two-step tuning method to train the model. The method incorporates user/item ID fields in prompts and employs a conventional collaborative model to generate user/item representations. CoLLM is built upon MiniGPT-4 and utilizes pretrained Vicuna weights for training.

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.

Biomni is a general-purpose biomedical AI agent designed to autonomously execute a wide range of research tasks across diverse biomedical subfields. By integrating cutting-edge large language model (LLM) reasoning with retrieval-augmented planning and code-based execution, Biomni helps scientists dramatically enhance research productivity and generate testable hypotheses.