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.

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.

The TensorRT-LLM Backend is a Triton backend designed to serve TensorRT-LLM models with Triton Inference Server. It supports features like inflight batching, paged attention, and more. Users can access the backend through pre-built Docker containers or build it using scripts provided in the repository. The backend can be used to create models for tasks like tokenizing, inferencing, de-tokenizing, ensemble modeling, and more. Users can interact with the backend using provided client scripts and query the server for metrics related to request handling, memory usage, KV cache blocks, and more. Testing for the backend can be done following the instructions in the 'ci/README.md' file.

ZipNN is a lossless and near-lossless compression library optimized for numbers/tensors in the Foundation Models environment. It automatically prepares data for compression based on its type, allowing users to focus on core tasks without worrying about compression complexities. The library delivers effective compression techniques for different data types and structures, achieving high compression ratios and rates. ZipNN supports various compression methods like ZSTD, lz4, and snappy, and provides ready-made scripts for file compression/decompression. Users can also manually import the package to compress and decompress data. The library offers advanced configuration options for customization and validation tests for different input and compression types.

LLM Finetuning toolkit is a config-based CLI tool for launching a series of LLM fine-tuning experiments on your data and gathering their results. It allows users to control all elements of a typical experimentation pipeline - prompts, open-source LLMs, optimization strategy, and LLM testing - through a single YAML configuration file. The toolkit supports basic, intermediate, and advanced usage scenarios, enabling users to run custom experiments, conduct ablation studies, and automate fine-tuning workflows. It provides features for data ingestion, model definition, training, inference, quality assurance, and artifact outputs, making it a comprehensive tool for fine-tuning large language models.

The Lakera PINT Benchmark provides a neutral evaluation method for prompt injection detection systems, offering a dataset of English inputs with prompt injections, jailbreaks, benign inputs, user-agent chats, and public document excerpts. The dataset is designed to be challenging and representative, with plans for future enhancements. The benchmark aims to be unbiased and accurate, welcoming contributions to improve prompt injection detection. Users can evaluate prompt injection detection systems using the provided Jupyter Notebook. The dataset structure is specified in YAML format, allowing users to prepare their datasets for benchmarking. Evaluation examples and resources are provided to assist users in evaluating prompt injection detection models and tools.

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.

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).

This repository contains code for research conducted by the LLM-Random research group at IDEAS NCBR in Warsaw, Poland. The group focuses on developing and using this repository to conduct research. For more information about the group and its research, refer to their blog, llm-random.github.io.

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.

LazyLLM is a low-code development tool for building complex AI applications with multiple agents. It assists developers in building AI applications at a low cost and continuously optimizing their performance. The tool provides a convenient workflow for application development and offers standard processes and tools for various stages of application development. Users can quickly prototype applications with LazyLLM, analyze bad cases with scenario task data, and iteratively optimize key components to enhance the overall application performance. LazyLLM aims to simplify the AI application development process and provide flexibility for both beginners and experts to create high-quality applications.

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.

LLM-on-Ray is a comprehensive solution for building, customizing, and deploying Large Language Models (LLMs). It simplifies complex processes into manageable steps by leveraging the power of Ray for distributed computing. The tool supports pretraining, finetuning, and serving LLMs across various hardware setups, incorporating industry and Intel optimizations for performance. It offers modular workflows with intuitive configurations, robust fault tolerance, and scalability. Additionally, it provides an Interactive Web UI for enhanced usability, including a chatbot application for testing and refining models.

Sarathi-Serve is the official OSDI'24 artifact submission for paper #444, focusing on 'Taming Throughput-Latency Tradeoff in LLM Inference'. It is a research prototype built on top of CUDA 12.1, designed to optimize throughput-latency tradeoff in Large Language Models (LLM) inference. The tool provides a Python environment for users to install and reproduce results from the associated experiments. Users can refer to specific folders for individual figures and are encouraged to cite the paper if they use the tool in their work.

CodiumAI Cover Agent is a tool designed to help increase code coverage by automatically generating qualified tests to enhance existing test suites. It utilizes Generative AI to streamline development workflows and is part of a suite of utilities aimed at automating the creation of unit tests for software projects. The system includes components like Test Runner, Coverage Parser, Prompt Builder, and AI Caller to simplify and expedite the testing process, ensuring high-quality software development. Cover Agent can be run via a terminal and is planned to be integrated into popular CI platforms. The tool outputs debug files locally, such as generated_prompt.md, run.log, and test_results.html, providing detailed information on generated tests and their status. It supports multiple LLMs and allows users to specify the model to use for test generation.

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.

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.