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.

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.

FlashInfer is a library for Language Languages Models that provides high-performance implementation of LLM GPU kernels such as FlashAttention, PageAttention and LoRA. FlashInfer focus on LLM serving and inference, and delivers state-the-art performance across diverse scenarios.

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.

RLAIF-V is a novel framework that aligns MLLMs in a fully open-source paradigm for super GPT-4V trustworthiness. It maximally exploits open-source feedback from high-quality feedback data and online feedback learning algorithm. Notable features include achieving super GPT-4V trustworthiness in both generative and discriminative tasks, using high-quality generalizable feedback data to reduce hallucination of different MLLMs, and exhibiting better learning efficiency and higher performance through iterative alignment.

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.

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.

dLLM-RL is a revolutionary reinforcement learning framework designed for Diffusion Large Language Models. It supports various models with diverse structures, offers inference acceleration, RL training capabilities, and SFT functionalities. The tool introduces TraceRL for trajectory-aware RL and diffusion-based value models for optimization stability. Users can download and try models like TraDo-4B-Instruct and TraDo-8B-Instruct. The tool also provides support for multi-node setups and easy building of reinforcement learning methods. Additionally, it offers supervised fine-tuning strategies for different models and tasks.

Data-Juicer is a one-stop data processing system to make data higher-quality, juicier, and more digestible for LLMs. It is a systematic & reusable library of 80+ core OPs, 20+ reusable config recipes, and 20+ feature-rich dedicated toolkits, designed to function independently of specific LLM datasets and processing pipelines. Data-Juicer allows detailed data analyses with an automated report generation feature for a deeper understanding of your dataset. Coupled with multi-dimension automatic evaluation capabilities, it supports a timely feedback loop at multiple stages in the LLM development process. Data-Juicer offers tens of pre-built data processing recipes for pre-training, fine-tuning, en, zh, and more scenarios. It provides a speedy data processing pipeline requiring less memory and CPU usage, optimized for maximum productivity. Data-Juicer is flexible & extensible, accommodating most types of data formats and allowing flexible combinations of OPs. It is designed for simplicity, with comprehensive documentation, easy start guides and demo configs, and intuitive configuration with simple adding/removing OPs from existing configs.

Holmes-VAD is a framework for unbiased and explainable Video Anomaly Detection using multimodal instructions. It addresses biased detection in challenging events by leveraging precise temporal supervision and rich multimodal instructions. The framework includes a largescale VAD instruction-tuning benchmark, VAD-Instruct50k, created with single-frame annotations and a robust video captioner. It offers accurate anomaly localization and comprehensive explanations through a customized solution for interpretable video anomaly detection.

Stellar Chat is a multi-modal chat application that enables users to create custom agents and integrate with local language models and OpenAI models. It provides capabilities for generating images, visual recognition, text-to-speech, and speech-to-text functionalities. Users can engage in multimodal conversations, create custom agents, search messages and conversations, and integrate with various applications for enhanced productivity. The project is part of the '100 Commits' competition, challenging participants to make meaningful commits daily for 100 consecutive days.

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.

Grounded-VideoLLM is a Video Large Language Model specialized in fine-grained temporal grounding. It excels in tasks such as temporal sentence grounding, dense video captioning, and grounded VideoQA. The model incorporates an additional temporal stream, discrete temporal tokens with specific time knowledge, and a multi-stage training scheme. It shows potential as a versatile video assistant for general video understanding. The repository provides pretrained weights, inference scripts, and datasets for training. Users can run inference queries to get temporal information from videos and train the model from scratch.

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.