ToolUniverse is a collection of 211 biomedical tools designed for Agentic AI, providing access to biomedical knowledge for solving therapeutic reasoning tasks. The tools cover various aspects of drugs and diseases, linked to trusted sources like US FDA-approved drugs since 1939, Open Targets, and Monarch Initiative.

LionAGI is a powerful intelligent workflow automation framework that introduces advanced ML models into any existing workflows and data infrastructure. It can interact with almost any model, run interactions in parallel for most models, produce structured pydantic outputs with flexible usage, automate workflow via graph based agents, use advanced prompting techniques, and more. LionAGI aims to provide a centralized agent-managed framework for "ML-powered tools coordination" and to dramatically lower the barrier of entries for creating use-case/domain specific tools. It is designed to be asynchronous only and requires Python 3.10 or higher.

EcoLogits tracks energy consumption and environmental impacts of generative AI models through APIs. It provides estimated environmental impacts of the inference, such as energy consumption and GHG emissions. The tool supports integration with various providers like Anthropic, Cohere, Google GenerativeAI, Huggingface Hub, MistralAI, and OpenAI. Users can easily install EcoLogits using pip and access detailed documentation on ecologits.ai. The project welcomes contributions and is licensed under MPL-2.0.

LightRAG is a PyTorch library designed for building and optimizing Retriever-Agent-Generator (RAG) pipelines. It follows principles of simplicity, quality, and optimization, offering developers maximum customizability with minimal abstraction. The library includes components for model interaction, output parsing, and structured data generation. LightRAG facilitates tasks like providing explanations and examples for concepts through a question-answering pipeline.

mlx-llm is a library that allows you to run Large Language Models (LLMs) on Apple Silicon devices in real-time using Apple's MLX framework. It provides a simple and easy-to-use API for creating, loading, and using LLM models, as well as a variety of applications such as chatbots, fine-tuning, and retrieval-augmented generation.

ShannonBase is a HTAP database provided by Shannon Data AI, designed for big data and AI. It extends MySQL with native embedding support, machine learning capabilities, a JavaScript engine, and a columnar storage engine. ShannonBase supports multimodal data types and natively integrates LightGBM for training and prediction. It leverages embedding algorithms and vector data type for ML/RAG tasks, providing Zero Data Movement, Native Performance Optimization, and Seamless SQL Integration. The tool includes a lightweight JavaScript engine for writing stored procedures in SQL or JavaScript.

RAGoon is a high-level library designed for batched embeddings generation, fast web-based RAG (Retrieval-Augmented Generation) processing, and quantized indexes processing. It provides NLP utilities for multi-model embedding production, high-dimensional vector visualization, and enhancing language model performance through search-based querying, web scraping, and data augmentation techniques.

SenseVoice is a speech foundation model focusing on high-accuracy multilingual speech recognition, speech emotion recognition, and audio event detection. Trained with over 400,000 hours of data, it supports more than 50 languages and excels in emotion recognition and sound event detection. The model offers efficient inference with low latency and convenient finetuning scripts. It can be deployed for service with support for multiple client-side languages. SenseVoice-Small model is open-sourced and provides capabilities for Mandarin, Cantonese, English, Japanese, and Korean. The tool also includes features for natural speech generation and fundamental speech recognition tasks.

Instructor Go is a library that simplifies working with structured outputs from large language models (LLMs). Built on top of `invopop/jsonschema` and utilizing `jsonschema` Go struct tags, it provides a user-friendly API for managing validation, retries, and streaming responses without changing code logic. The library supports LLM provider APIs such as OpenAI, Anthropic, Cohere, and Google, capturing and returning usage data in responses. Users can easily add metadata to struct fields using `jsonschema` tags to enhance model awareness and streamline workflows.

Build fast and accurate GenAI applications with GraphRAG SDK, a specialized toolkit for building Graph Retrieval-Augmented Generation (GraphRAG) systems. It integrates knowledge graphs, ontology management, and state-of-the-art LLMs to deliver accurate, efficient, and customizable RAG workflows. The SDK simplifies the development process by automating ontology creation, knowledge graph agent creation, and query handling, enabling users to interact and query their knowledge graphs effectively. It supports multi-agent systems and orchestrates agents specialized in different domains. The SDK is optimized for FalkorDB, ensuring high performance and scalability for large-scale applications. By leveraging knowledge graphs, it enables semantic relationships and ontology-driven queries that go beyond standard vector similarity, enhancing retrieval-augmented generation capabilities.

Redis Vector Library (RedisVL) is a Python client library for building AI applications on top of Redis. It provides a high-level interface for managing vector indexes, performing vector search, and integrating with popular embedding models and providers. RedisVL is designed to make it easy for developers to build and deploy AI applications that leverage the speed, flexibility, and reliability of Redis.

mcp-agent is a simple, composable framework designed to build agents using the Model Context Protocol. It handles the lifecycle of MCP server connections and implements patterns for building production-ready AI agents in a composable way. The framework also includes OpenAI's Swarm pattern for multi-agent orchestration in a model-agnostic manner, making it the simplest way to build robust agent applications. It is purpose-built for the shared protocol MCP, lightweight, and closer to an agent pattern library than a framework. mcp-agent allows developers to focus on the core business logic of their AI applications by handling mechanics such as server connections, working with LLMs, and supporting external signals like human input.

Phi-3-MLX is a versatile AI framework that leverages both the Phi-3-Vision multimodal model and the Phi-3-Mini-128K language model optimized for Apple Silicon using the MLX framework. It provides an easy-to-use interface for a wide range of AI tasks, from advanced text generation to visual question answering and code execution. The project features support for batched generation, flexible agent system, custom toolchains, model quantization, LoRA fine-tuning capabilities, and API integration for extended functionality.

ChatRex is a Multimodal Large Language Model (MLLM) designed to seamlessly integrate fine-grained object perception and robust language understanding. By adopting a decoupled architecture with a retrieval-based approach for object detection and leveraging high-resolution visual inputs, ChatRex addresses key challenges in perception tasks. It is powered by the Rexverse-2M dataset with diverse image-region-text annotations. ChatRex can be applied to various scenarios requiring fine-grained perception, such as object detection, grounded conversation, grounded image captioning, and region understanding.

xLSTM is a new Recurrent Neural Network architecture based on ideas of the original LSTM. Through Exponential Gating with appropriate normalization and stabilization techniques and a new Matrix Memory it overcomes the limitations of the original LSTM and shows promising performance on Language Modeling when compared to Transformers or State Space Models. The package is based on PyTorch and was tested for versions >=1.8. For the CUDA version of xLSTM, you need Compute Capability >= 8.0. The xLSTM tool provides two main components: xLSTMBlockStack for non-language applications or integrating in other architectures, and xLSTMLMModel for language modeling or other token-based applications.

RAID is the largest and most comprehensive dataset for evaluating AI-generated text detectors. It contains over 10 million documents spanning 11 LLMs, 11 genres, 4 decoding strategies, and 12 adversarial attacks. RAID is designed to be the go-to location for trustworthy third-party evaluation of popular detectors. The dataset covers diverse models, domains, sampling strategies, and attacks, making it a valuable resource for training detectors, evaluating generalization, protecting against adversaries, and comparing to state-of-the-art models from academia and industry.

PINNACLE is a flexible geometric deep learning approach that trains on contextualized protein interaction networks to generate context-aware protein representations. It provides protein representations split across various cell-type contexts from different tissues and organs. The tool can be fine-tuned to study the genomic effects of drugs and nominate promising protein targets and cell-type contexts for further investigation. PINNACLE exemplifies the paradigm of incorporating context-specific effects for studying biological systems, especially the impact of disease and therapeutics.

ToolUniverse is a collection of 211 biomedical tools designed for Agentic AI, providing access to biomedical knowledge for solving therapeutic reasoning tasks. The tools cover various aspects of drugs and diseases, linked to trusted sources like US FDA-approved drugs since 1939, Open Targets, and Monarch Initiative.

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.

Scientific Large Language Models (Sci-LLMs) is a repository that collects papers on scientific large language models, focusing on biology and chemistry domains. It includes textual, molecular, protein, and genomic languages, as well as multimodal language. The repository covers various large language models for tasks such as molecule property prediction, interaction prediction, protein sequence representation, protein sequence generation/design, DNA-protein interaction prediction, and RNA prediction. It also provides datasets and benchmarks for evaluating these models. The repository aims to facilitate research and development in the field of scientific language modeling.

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.

cellseg-models.pytorch is a Python library built upon PyTorch for 2D cell/nuclei instance segmentation models. It provides multi-task encoder-decoder architectures and post-processing methods for segmenting cell/nuclei instances. The library offers high-level API to define segmentation models, open-source datasets for training, flexibility to modify model components, sliding window inference, multi-GPU inference, benchmarking utilities, regularization techniques, and example notebooks for training and finetuning models with different backbones.

AICSImageIO is a Python tool for Image Reading, Metadata Conversion, and Image Writing for Microscopy Images. It supports various file formats like OME-TIFF, TIFF, ND2, DV, CZI, LIF, PNG, GIF, and Bio-Formats. Users can read and write metadata and imaging data, work with different file systems like local paths, HTTP URLs, s3fs, and gcsfs. The tool provides functionalities for full image reading, delayed image reading, mosaic image reading, metadata reading, xarray coordinate plane attachment, cloud IO support, and saving to OME-TIFF. It also offers benchmarking and developer resources.

ceLLama is a streamlined automation pipeline for cell type annotations using large-language models (LLMs). It operates locally to ensure privacy, provides comprehensive analysis by considering negative genes, offers efficient processing speed, and generates customized reports. Ideal for quick and preliminary cell type checks.

PINNACLE is a flexible geometric deep learning approach that trains on contextualized protein interaction networks to generate context-aware protein representations. It provides protein representations split across various cell-type contexts from different tissues and organs. The tool can be fine-tuned to study the genomic effects of drugs and nominate promising protein targets and cell-type contexts for further investigation. PINNACLE exemplifies the paradigm of incorporating context-specific effects for studying biological systems, especially the impact of disease and therapeutics.

Taiyi (太一) is a bilingual large language model fine-tuned for diverse biomedical tasks. It aims to facilitate communication between healthcare professionals and patients, provide medical information, and assist in diagnosis, biomedical knowledge discovery, drug development, and personalized healthcare solutions. The model is based on the Qwen-7B-base model and has been fine-tuned using rich bilingual instruction data. It covers tasks such as question answering, biomedical dialogue, medical report generation, biomedical information extraction, machine translation, title generation, text classification, and text semantic similarity. The project also provides standardized data formats, model training details, model inference guidelines, and overall performance metrics across various BioNLP tasks.