KG_RAG

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.

Chitu is a high-performance inference framework for large language models, focusing on efficiency, flexibility, and availability. It supports various mainstream large language models, including DeepSeek, LLaMA series, Mixtral, and more. Chitu integrates latest optimizations for large language models, provides efficient operators with online FP8 to BF16 conversion, and is deployed for real-world production. The framework is versatile, supporting various hardware environments beyond NVIDIA GPUs. Chitu aims to enhance output speed per unit computing power, especially in decoding processes dependent on memory bandwidth.

Gemma is a family of open-weights Large Language Model (LLM) by Google DeepMind, based on Gemini research and technology. This repository contains an inference implementation and examples, based on the Flax and JAX frameworks. Gemma can run on CPU, GPU, and TPU, with model checkpoints available for download. It provides tutorials, reference implementations, and Colab notebooks for tasks like sampling and fine-tuning. Users can contribute to Gemma through bug reports and pull requests. The code is licensed under the Apache License, Version 2.0.

Model2Vec is a technique to turn any sentence transformer into a really small static model, reducing model size by 15x and making the models up to 500x faster, with a small drop in performance. It outperforms other static embedding models like GLoVe and BPEmb, is lightweight with only `numpy` as a major dependency, offers fast inference, dataset-free distillation, and is integrated into Sentence Transformers, txtai, and Chonkie. Model2Vec creates powerful models by passing a vocabulary through a sentence transformer model, reducing dimensionality using PCA, and weighting embeddings using zipf weighting. Users can distill their own models or use pre-trained models from the HuggingFace hub. Evaluation can be done using the provided evaluation package. Model2Vec is licensed under MIT.

NeMo Curator is a GPU-accelerated open-source framework designed for efficient large language model data curation. It provides scalable dataset preparation for tasks like foundation model pretraining, domain-adaptive pretraining, supervised fine-tuning, and parameter-efficient fine-tuning. The library leverages GPUs with Dask and RAPIDS to accelerate data curation, offering customizable and modular interfaces for pipeline expansion and model convergence. Key features include data download, text extraction, quality filtering, deduplication, downstream-task decontamination, distributed data classification, and PII redaction. NeMo Curator is suitable for curating high-quality datasets for large language model training.

CompressAI-Vision is a tool that helps you develop, test, and evaluate compression models with standardized tests in the context of compression methods optimized for machine tasks algorithms such as Neural-Network (NN)-based detectors. It currently focuses on two types of pipeline: Video compression for remote inference (`compressai-remote-inference`), which corresponds to the MPEG "Video Coding for Machines" (VCM) activity. Split inference (`compressai-split-inference`), which includes an evaluation framework for compressing intermediate features produced in the context of split models. The software supports all the pipelines considered in the related MPEG activity: "Feature Compression for Machines" (FCM).

DemoGPT is an all-in-one agent library that provides tools, prompts, frameworks, and LLM models for streamlined agent development. It leverages GPT-3.5-turbo to generate LangChain code, creating interactive Streamlit applications. The tool is designed for creating intelligent, interactive, and inclusive solutions in LLM-based application development. It offers model flexibility, iterative development, and a commitment to user engagement. Future enhancements include integrating Gorilla for autonomous API usage and adding a publicly available database for refining the generation process.

FunClip is an open-source, locally deployable automated video editing tool that utilizes the FunASR Paraformer series models from Alibaba DAMO Academy for speech recognition in videos. Users can select text segments or speakers from the recognition results and click the clip button to obtain the corresponding video segments. FunClip integrates advanced features such as the Paraformer-Large model for accurate Chinese ASR, SeACo-Paraformer for customized hotword recognition, CAM++ speaker recognition model, Gradio interactive interface for easy usage, support for multiple free edits with automatic SRT subtitles generation, and segment-specific SRT subtitles.

This repository contains the training and inference code needed to replicate the winning solution to the AI Mathematical Olympiad - Progress Prize 1. It consists of fine-tuning DeepSeekMath-Base 7B, high-quality training datasets, a self-consistency decoding algorithm, and carefully chosen validation sets. The training methodology involves Chain of Thought (CoT) and Tool Integrated Reasoning (TIR) training stages. Two datasets, NuminaMath-CoT and NuminaMath-TIR, were used to fine-tune the models. The models were trained using open-source libraries like TRL, PyTorch, vLLM, and DeepSpeed. Post-training quantization to 8-bit precision was done to improve performance on Kaggle's T4 GPUs. The project structure includes scripts for training, quantization, and inference, along with necessary installation instructions and hardware/software specifications.

ZenML is an extensible, open-source MLOps framework for creating portable, production-ready machine learning pipelines. By decoupling infrastructure from code, ZenML enables developers across your organization to collaborate more effectively as they develop to production.

The Open-Reasoning-Tasks repository is a collaborative project aimed at creating a comprehensive list of reasoning tasks for training large language models (LLMs). Contributors can submit tasks with descriptions, examples, and optional diagrams to enhance LLMs' reasoning capabilities.

The development of Natural Language Interfaces to Databases (NLIDBs) has been greatly advanced by the advent of large language models (LLMs), which provide an intuitive way to translate natural language (NL) questions into Structured Query Language (SQL) queries. DBCopilot is a framework that addresses challenges in real-world scenarios of natural language querying over massive databases by employing a compact and flexible copilot model for routing. It decouples schema-agnostic NL2SQL into schema routing and SQL generation, utilizing a lightweight differentiable search index for semantic mappings and relation-aware joint retrieval. DBCopilot introduces a reverse schema-to-question generation paradigm for automatic learning and adaptation over massive databases, providing a scalable and effective solution for schema-agnostic NL2SQL.

NineRec is a benchmark dataset suite for evaluating transferable recommendation models. It provides datasets for pre-training and transfer learning in recommender systems, focusing on multimodal and foundation model tasks. The dataset includes user-item interactions, item texts in multiple languages, item URLs, and raw images. Researchers can use NineRec to develop more effective and efficient methods for pre-training recommendation models beyond end-to-end training. The dataset is accompanied by code for dataset preparation, training, and testing in PyTorch environment.

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.

CALF (LLaTA) is a cross-modal fine-tuning framework that bridges the distribution discrepancy between temporal data and the textual nature of LLMs. It introduces three cross-modal fine-tuning techniques: Cross-Modal Match Module, Feature Regularization Loss, and Output Consistency Loss. The framework aligns time series and textual inputs, ensures effective weight updates, and maintains consistent semantic context for time series data. CALF provides scripts for long-term and short-term forecasting, requires Python 3.9, and utilizes word token embeddings for model training.

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.

LLMStack is a no-code platform for building generative AI agents, workflows, and chatbots. It allows users to connect their own data, internal tools, and GPT-powered models without any coding experience. LLMStack can be deployed to the cloud or on-premise and can be accessed via HTTP API or triggered from Slack or Discord.

This guide is dedicated to Large Language Models (LLMs) that you can run on your home computer. It assumes your PC is a lower-end, non-gaming setup.

ONNX Runtime Generative AI is a library that provides the generative AI loop for ONNX models, including inference with ONNX Runtime, logits processing, search and sampling, and KV cache management. Users can call a high level `generate()` method, or run each iteration of the model in a loop. It supports greedy/beam search and TopP, TopK sampling to generate token sequences, has built in logits processing like repetition penalties, and allows for easy custom scoring.

Jupyter AI connects generative AI with Jupyter notebooks. It provides a user-friendly and powerful way to explore generative AI models in notebooks and improve your productivity in JupyterLab and the Jupyter Notebook. Specifically, Jupyter AI offers: * An `%%ai` magic that turns the Jupyter notebook into a reproducible generative AI playground. This works anywhere the IPython kernel runs (JupyterLab, Jupyter Notebook, Google Colab, Kaggle, VSCode, etc.). * A native chat UI in JupyterLab that enables you to work with generative AI as a conversational assistant. * Support for a wide range of generative model providers, including AI21, Anthropic, AWS, Cohere, Gemini, Hugging Face, NVIDIA, and OpenAI. * Local model support through GPT4All, enabling use of generative AI models on consumer grade machines with ease and privacy.

Khoj is an open-source, personal AI assistant that extends your capabilities by creating always-available AI agents. You can share your notes and documents to extend your digital brain, and your AI agents have access to the internet, allowing you to incorporate real-time information. Khoj is accessible on Desktop, Emacs, Obsidian, Web, and Whatsapp, and you can share PDF, markdown, org-mode, notion files, and GitHub repositories. You'll get fast, accurate semantic search on top of your docs, and your agents can create deeply personal images and understand your speech. Khoj is self-hostable and always will be.

LangChain.dart is a Dart port of the popular LangChain Python framework created by Harrison Chase. LangChain provides a set of ready-to-use components for working with language models and a standard interface for chaining them together to formulate more advanced use cases (e.g. chatbots, Q&A with RAG, agents, summarization, extraction, etc.). The components can be grouped into a few core modules: * **Model I/O:** LangChain offers a unified API for interacting with various LLM providers (e.g. OpenAI, Google, Mistral, Ollama, etc.), allowing developers to switch between them with ease. Additionally, it provides tools for managing model inputs (prompt templates and example selectors) and parsing the resulting model outputs (output parsers). * **Retrieval:** assists in loading user data (via document loaders), transforming it (with text splitters), extracting its meaning (using embedding models), storing (in vector stores) and retrieving it (through retrievers) so that it can be used to ground the model's responses (i.e. Retrieval-Augmented Generation or RAG). * **Agents:** "bots" that leverage LLMs to make informed decisions about which available tools (such as web search, calculators, database lookup, etc.) to use to accomplish the designated task. The different components can be composed together using the LangChain Expression Language (LCEL).

Danswer is an open-source Gen-AI Chat and Unified Search tool that connects to your company's docs, apps, and people. It provides a Chat interface and plugs into any LLM of your choice. Danswer can be deployed anywhere and for any scale - on a laptop, on-premise, or to cloud. Since you own the deployment, your user data and chats are fully in your own control. Danswer is MIT licensed and designed to be modular and easily extensible. The system also comes fully ready for production usage with user authentication, role management (admin/basic users), chat persistence, and a UI for configuring Personas (AI Assistants) and their Prompts. Danswer also serves as a Unified Search across all common workplace tools such as Slack, Google Drive, Confluence, etc. By combining LLMs and team specific knowledge, Danswer becomes a subject matter expert for the team. Imagine ChatGPT if it had access to your team's unique knowledge! It enables questions such as "A customer wants feature X, is this already supported?" or "Where's the pull request for feature Y?"

Infinity is an AI-native database designed for LLM applications, providing incredibly fast full-text and vector search capabilities. It supports a wide range of data types, including vectors, full-text, and structured data, and offers a fused search feature that combines multiple embeddings and full text. Infinity is easy to use, with an intuitive Python API and a single-binary architecture that simplifies deployment. It achieves high performance, with 0.1 milliseconds query latency on million-scale vector datasets and up to 15K QPS.

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.