TxAgent is an AI agent designed for precision therapeutics, leveraging multi-step reasoning and real-time biomedical knowledge retrieval across a toolbox of 211 tools. It evaluates drug interactions, contraindications, and tailors treatment strategies to individual patient characteristics. TxAgent outperforms leading models across various drug reasoning tasks and personalized treatment scenarios, ensuring treatment recommendations align with clinical guidelines and real-world evidence.

rLLM is an open-source framework for post-training language agents via reinforcement learning. With rLLM, you can easily build your custom agents and environments, train them with reinforcement learning, and deploy them for real-world workloads. The framework provides tools for training coding models, software engineering agents, and language agents using reinforcement learning techniques. It supports various models of different sizes and capabilities, enabling users to achieve state-of-the-art performance in coding and language-related tasks. rLLM is designed to be user-friendly, scalable, and efficient for training and deploying language agents in diverse applications.

SeerAttention is a novel trainable sparse attention mechanism that learns intrinsic sparsity patterns directly from LLMs through self-distillation at post-training time. It achieves faster inference while maintaining accuracy for long-context prefilling. The tool offers features such as trainable sparse attention, block-level sparsity, self-distillation, efficient kernel, and easy integration with existing transformer architectures. Users can quickly start using SeerAttention for inference with AttnGate Adapter and training attention gates with self-distillation. The tool provides efficient evaluation methods and encourages contributions from the community.

FATE-LLM is a framework supporting federated learning for large and small language models. It promotes training efficiency of federated LLMs using Parameter-Efficient methods, protects the IP of LLMs using FedIPR, and ensures data privacy during training and inference through privacy-preserving mechanisms.

CuMo is a project focused on scaling multimodal Large Language Models (LLMs) with Co-Upcycled Mixture-of-Experts. It introduces CuMo, which incorporates Co-upcycled Top-K sparsely-gated Mixture-of-experts blocks into the vision encoder and the MLP connector, enhancing the capabilities of multimodal LLMs. The project adopts a three-stage training approach with auxiliary losses to stabilize the training process and maintain a balanced loading of experts. CuMo achieves comparable performance to other state-of-the-art multimodal LLMs on various Visual Question Answering (VQA) and visual-instruction-following benchmarks.

ALMA (Advanced Language Model-based Translator) is a many-to-many LLM-based translation model that utilizes a two-step fine-tuning process on monolingual and parallel data to achieve strong translation performance. ALMA-R builds upon ALMA models with LoRA fine-tuning and Contrastive Preference Optimization (CPO) for even better performance, surpassing GPT-4 and WMT winners. The repository provides ALMA and ALMA-R models, datasets, environment setup, evaluation scripts, training guides, and data information for users to leverage these models for translation tasks.

Vision-LLM-Alignment is a repository focused on implementing alignment training for visual large language models (LLMs), including SFT training, reward model training, and PPO/DPO training. It supports various model architectures and provides datasets for training. The repository also offers benchmark results and installation instructions for users.

Slideflow is a deep learning library for digital pathology, offering a user-friendly interface for model development. It is designed for medical researchers and AI enthusiasts, providing an accessible platform for developing state-of-the-art pathology models. Slideflow offers customizable training pipelines, robust slide processing and stain normalization toolkit, support for weakly-supervised or strongly-supervised labels, built-in foundation models, multiple-instance learning, self-supervised learning, generative adversarial networks, explainability tools, layer activation analysis tools, uncertainty quantification, interactive user interface for model deployment, and more. It supports both PyTorch and Tensorflow, with optional support for Libvips for slide reading. Slideflow can be installed via pip, Docker container, or from source, and includes non-commercial add-ons for additional tools and pretrained models. It allows users to create projects, extract tiles from slides, train models, and provides evaluation tools like heatmaps and mosaic maps.

CRAB is a framework for building LLM agent benchmark environments in a Python-centric way. It is cross-platform and multi-environment, allowing the creation of agent environments supporting various deployment options. The framework offers easy-to-use configuration with the ability to add new actions and define environments seamlessly. CRAB also provides a novel benchmarking suite with tasks and evaluators defined in Python, along with a unique graph evaluator method for detailed metrics.

Raga LLM Hub is a comprehensive evaluation toolkit for Language and Learning Models (LLMs) with over 100 meticulously designed metrics. It allows developers and organizations to evaluate and compare LLMs effectively, establishing guardrails for LLMs and Retrieval Augmented Generation (RAG) applications. The platform assesses aspects like Relevance & Understanding, Content Quality, Hallucination, Safety & Bias, Context Relevance, Guardrails, and Vulnerability scanning, along with Metric-Based Tests for quantitative analysis. It helps teams identify and fix issues throughout the LLM lifecycle, revolutionizing reliability and trustworthiness.

This repository, MMC, focuses on advancing multimodal chart understanding through large-scale instruction tuning. It introduces a dataset supporting various tasks and chart types, a benchmark for evaluating reasoning capabilities over charts, and an assistant achieving state-of-the-art performance on chart QA benchmarks. The repository provides data for chart-text alignment, benchmarking, and instruction tuning, along with existing datasets used in experiments. Additionally, it offers a Gradio demo for the MMCA model.

Ichigo is a local real-time voice AI tool that uses an early fusion technique to extend a text-based LLM to have native 'listening' ability. It is an open research experiment with improved multiturn capabilities and the ability to refuse processing inaudible queries. The tool is designed for open data, open weight, on-device Siri-like functionality, inspired by Meta's Chameleon paper. Ichigo offers a web UI demo and Gradio web UI for users to interact with the tool. It has achieved enhanced MMLU scores, stronger context handling, advanced noise management, and improved multi-turn capabilities for a robust user experience.

EmbodiedScan is a holistic multi-modal 3D perception suite designed for embodied AI. It introduces a multi-modal, ego-centric 3D perception dataset and benchmark for holistic 3D scene understanding. The dataset includes over 5k scans with 1M ego-centric RGB-D views, 1M language prompts, 160k 3D-oriented boxes spanning 760 categories, and dense semantic occupancy with 80 common categories. The suite includes a baseline framework named Embodied Perceptron, capable of processing multi-modal inputs for 3D perception tasks and language-grounded tasks.

PowerInfer is a high-speed Large Language Model (LLM) inference engine designed for local deployment on consumer-grade hardware, leveraging activation locality to optimize efficiency. It features a locality-centric design, hybrid CPU/GPU utilization, easy integration with popular ReLU-sparse models, and support for various platforms. PowerInfer achieves high speed with lower resource demands and is flexible for easy deployment and compatibility with existing models like Falcon-40B, Llama2 family, ProSparse Llama2 family, and Bamboo-7B.

Atom is an accurate low-bit weight-activation quantization algorithm that combines mixed-precision, fine-grained group quantization, dynamic activation quantization, KV-cache quantization, and efficient CUDA kernels co-design. It introduces a low-bit quantization method, Atom, to maximize Large Language Models (LLMs) serving throughput with negligible accuracy loss. The codebase includes evaluation of perplexity and zero-shot accuracy, kernel benchmarking, and end-to-end evaluation. Atom significantly boosts serving throughput by using low-bit operators and reduces memory consumption via low-bit quantization.

AdalFlow is a library designed to help developers build and optimize Large Language Model (LLM) task pipelines. It follows a design pattern similar to PyTorch, offering a light, modular, and robust codebase. Named in honor of Ada Lovelace, AdalFlow aims to inspire more women to enter the AI field. The library is tailored for various GenAI applications like chatbots, translation, summarization, code generation, and autonomous agents, as well as classical NLP tasks such as text classification and named entity recognition. AdalFlow emphasizes modularity, robustness, and readability to support users in customizing and iterating code for their specific use cases.

TxAgent is an AI agent designed for precision therapeutics, leveraging multi-step reasoning and real-time biomedical knowledge retrieval across a toolbox of 211 tools. It evaluates drug interactions, contraindications, and tailors treatment strategies to individual patient characteristics. TxAgent outperforms leading models across various drug reasoning tasks and personalized treatment scenarios, ensuring treatment recommendations align with clinical guidelines and real-world evidence.

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.