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.

InfLLM is a training-free memory-based method that unveils the intrinsic ability of LLMs to process streaming long sequences. It stores distant contexts into additional memory units and employs an efficient mechanism to lookup token-relevant units for attention computation. Thereby, InfLLM allows LLMs to efficiently process long sequences while maintaining the ability to capture long-distance dependencies. Without any training, InfLLM enables LLMs pre-trained on sequences of a few thousand tokens to achieve superior performance than competitive baselines continually training these LLMs on long sequences. Even when the sequence length is scaled to 1, 024K, InfLLM still effectively captures long-distance dependencies.

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.

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.

AI2BMD is a program for efficiently simulating protein molecular dynamics with ab initio accuracy. The repository contains datasets, simulation programs, and public materials related to AI2BMD. It provides a Docker image for easy deployment and a standalone launcher program. Users can run simulations by downloading the launcher script and specifying simulation parameters. The repository also includes ready-to-use protein structures for testing. AI2BMD is designed for x86-64 GNU/Linux systems with recommended hardware specifications. The related research includes model architectures like ViSNet, Geoformer, and fine-grained force metrics for MLFF. Citation information and contact details for the AI2BMD Team are provided.

Shards is a high-performance, multi-platform, type-safe programming language designed for visual development. It is a dataflow visual programming language that enables building full-fledged apps and games without traditional coding. Shards features automatic type checking, optimized shard implementations for high performance, and an intuitive visual workflow for beginners. The language allows seamless round-trip engineering between code and visual models, empowering users to create multi-platform apps easily. Shards also powers an upcoming AI-powered game creation system, enabling real-time collaboration and game development in a low to no-code environment.

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.

Do-Not-Answer is an open-source dataset curated to evaluate Large Language Models' safety mechanisms at a low cost. It consists of prompts to which responsible language models do not answer. The dataset includes human annotations and model-based evaluation using a fine-tuned BERT-like evaluator. The dataset covers 61 specific harms and collects 939 instructions across five risk areas and 12 harm types. Response assessment is done for six models, categorizing responses into harmfulness and action categories. Both human and automatic evaluations show the safety of models across different risk areas. The dataset also includes a Chinese version with 1,014 questions for evaluating Chinese LLMs' risk perception and sensitivity to specific words and phrases.

AI-Driven Research Assistant is an advanced AI-powered system utilizing specialized agents for data analysis, visualization, and report generation. It integrates LangChain, OpenAI's GPT models, and LangGraph for complex research processes. Key features include hypothesis generation, data processing, web search, code generation, and report writing. The system's unique Note Taker agent maintains project state, reducing overhead and improving context retention. System requirements include Python 3.10+ and Jupyter Notebook environment. Installation involves cloning the repository, setting up a Conda virtual environment, installing dependencies, and configuring environment variables. Usage instructions include setting data, running Jupyter Notebook, customizing research tasks, and viewing results. Main components include agents for hypothesis generation, process supervision, visualization, code writing, search, report writing, quality review, and note-taking. Workflow involves hypothesis generation, processing, quality review, and revision. Customization is possible by modifying agent creation and workflow definition. Current issues include OpenAI errors, NoteTaker efficiency, runtime optimization, and refiner improvement. Contributions via pull requests are welcome under the MIT License.

Wandbot is a question-answering bot designed for Weights & Biases documentation. It employs Retrieval Augmented Generation with a ChromaDB backend for efficient responses. The bot features periodic data ingestion, integration with Discord and Slack, and performance monitoring through logging. It has a fallback mechanism for model selection and is evaluated based on retrieval accuracy and model-generated responses. The implementation includes creating document embeddings, constructing the Q&A RAGPipeline, model selection, deployment on FastAPI, Discord, and Slack, logging and analysis with Weights & Biases Tables, and performance evaluation.

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 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.

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.

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.

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.