slideflow

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.

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.

Habitat-Lab is a modular high-level library for end-to-end development in embodied AI. It is designed to train agents to perform a wide variety of embodied AI tasks in indoor environments, as well as develop agents that can interact with humans in performing these tasks.

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.

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.

IPEX-LLM is a low-bit LLM library on Intel XPU (Xeon/Core/Flex/Arc/PVC) that provides tutorials to help users understand and use the library to build LLM applications. The tutorials cover topics such as introduction to IPEX-LLM, environment setup, basic application development, Chinese language support, intermediate and advanced application development, GPU acceleration, and finetuning. Users can learn how to build chat applications, chatbots, speech recognition, and more using IPEX-LLM.

Open-Source Evaluation for LLM Applications. `continuous-eval` is an open-source package created for granular and holistic evaluation of GenAI application pipelines. It offers modularized evaluation, a comprehensive metric library covering various LLM use cases, the ability to leverage user feedback in evaluation, and synthetic dataset generation for testing pipelines. Users can define their own metrics by extending the Metric class. The tool allows running evaluation on a pipeline defined with modules and corresponding metrics. Additionally, it provides synthetic data generation capabilities to create user interaction data for evaluation or training purposes.

Swiftide is a fast, streaming indexing and query library tailored for Retrieval Augmented Generation (RAG) in AI applications. It is built in Rust, utilizing parallel, asynchronous streams for blazingly fast performance. With Swiftide, users can easily build AI applications from idea to production in just a few lines of code. The tool addresses frustrations around performance, stability, and ease of use encountered while working with Python-based tooling. It offers features like fast streaming indexing pipeline, experimental query pipeline, integrations with various platforms, loaders, transformers, chunkers, embedders, and more. Swiftide aims to provide a platform for data indexing and querying to advance the development of automated Large Language Model (LLM) applications.

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.

Catalyst is a C# Natural Language Processing library designed for speed, inspired by spaCy's design. It provides pre-trained models, support for training word and document embeddings, and flexible entity recognition models. The library is fast, modern, and pure-C#, supporting .NET standard 2.0. It is cross-platform, running on Windows, Linux, macOS, and ARM. Catalyst offers non-destructive tokenization, named entity recognition, part-of-speech tagging, language detection, and efficient binary serialization. It includes pre-built models for language packages and lemmatization. Users can store and load models using streams. Getting started with Catalyst involves installing its NuGet Package and setting the storage to use the online repository. The library supports lazy loading of models from disk or online. Users can take advantage of C# lazy evaluation and native multi-threading support to process documents in parallel. Training a new FastText word2vec embedding model is straightforward, and Catalyst also provides algorithms for fast embedding search and dimensionality reduction.

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.

Rig is a Rust library designed for building scalable, modular, and user-friendly applications powered by large language models (LLMs). It provides full support for LLM completion and embedding workflows, offers simple yet powerful abstractions for LLM providers like OpenAI and Cohere, as well as vector stores such as MongoDB and in-memory storage. With Rig, users can easily integrate LLMs into their applications with minimal boilerplate code.

Nous is an open-source TypeScript platform for autonomous AI agents and LLM based workflows. It aims to automate processes, support requests, review code, assist with refactorings, and more. The platform supports various integrations, multiple LLMs/services, CLI and web interface, human-in-the-loop interactions, flexible deployment options, observability with OpenTelemetry tracing, and specific agents for code editing, software engineering, and code review. It offers advanced features like reasoning/planning, memory and function call history, hierarchical task decomposition, and control-loop function calling options. Nous is designed to be a flexible platform for the TypeScript community to expand and support different use cases and integrations.

InstructGraph is a framework designed to enhance large language models (LLMs) for graph-centric tasks by utilizing graph instruction tuning and preference alignment. The tool collects and decomposes 29 standard graph datasets into four groups, enabling LLMs to better understand and generate graph data. It introduces a structured format verbalizer to transform graph data into a code-like format, facilitating code understanding and generation. Additionally, it addresses hallucination problems in graph reasoning and generation through direct preference optimization (DPO). The tool aims to bridge the gap between textual LLMs and graph data, offering a comprehensive solution for graph-related tasks.

Sophia is an open-source TypeScript platform designed for autonomous AI agents and LLM based workflows. It aims to automate processes, review code, assist with refactorings, and support various integrations. The platform offers features like advanced autonomous agents, reasoning/planning inspired by Google's Self-Discover paper, memory and function call history, adaptive iterative planning, and more. Sophia supports multiple LLMs/services, CLI and web interface, human-in-the-loop interactions, flexible deployment options, observability with OpenTelemetry tracing, and specific agents for code editing, software engineering, and code review. It provides a flexible platform for the TypeScript community to expand and support various use cases and integrations.

The stable-diffusion.cpp repository provides an implementation for inferring stable diffusion in pure C/C++. It offers features such as support for different versions of stable diffusion, lightweight and dependency-free implementation, various quantization support, memory-efficient CPU inference, GPU acceleration, and more. Users can download the built executable program or build it manually. The repository also includes instructions for downloading weights, building from scratch, using different acceleration methods, running the tool, converting weights, and utilizing various features like Flash Attention, ESRGAN upscaling, PhotoMaker support, and more. Additionally, it mentions future TODOs and provides information on memory requirements, bindings, UIs, contributors, and references.

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.

This repository contains assets related to AI/ML workloads on Google Kubernetes Engine (GKE). Run optimized AI/ML workloads with Google Kubernetes Engine (GKE) platform orchestration capabilities. A robust AI/ML platform considers the following layers: Infrastructure orchestration that support GPUs and TPUs for training and serving workloads at scale Flexible integration with distributed computing and data processing frameworks Support for multiple teams on the same infrastructure to maximize utilization of resources

Ray is a unified framework for scaling AI and Python applications. It consists of a core distributed runtime and a set of AI libraries for simplifying ML compute, including Data, Train, Tune, RLlib, and Serve. Ray runs on any machine, cluster, cloud provider, and Kubernetes, and features a growing ecosystem of community integrations. With Ray, you can seamlessly scale the same code from a laptop to a cluster, making it easy to meet the compute-intensive demands of modern ML workloads.

Labelbox is a data-centric AI platform for enterprises to develop, optimize, and use AI to solve problems and power new products and services. Enterprises use Labelbox to curate data, generate high-quality human feedback data for computer vision and LLMs, evaluate model performance, and automate tasks by combining AI and human-centric workflows. The academic & research community uses Labelbox for cutting-edge AI research.

Deep Java Library (DJL) is an open-source, high-level, engine-agnostic Java framework for deep learning. It is designed to be easy to get started with and simple to use for Java developers. DJL provides a native Java development experience and allows users to integrate machine learning and deep learning models with their Java applications. The framework is deep learning engine agnostic, enabling users to switch engines at any point for optimal performance. DJL's ergonomic API interface guides users with best practices to accomplish deep learning tasks, such as running inference and training neural networks.

MLflow is a platform to streamline machine learning development, including tracking experiments, packaging code into reproducible runs, and sharing and deploying models. MLflow offers a set of lightweight APIs that can be used with any existing machine learning application or library (TensorFlow, PyTorch, XGBoost, etc), wherever you currently run ML code (e.g. in notebooks, standalone applications or the cloud). MLflow's current components are: * `MLflow Tracking `_: An API to log parameters, code, and results in machine learning experiments and compare them using an interactive UI. * `MLflow Projects `_: A code packaging format for reproducible runs using Conda and Docker, so you can share your ML code with others. * `MLflow Models `_: A model packaging format and tools that let you easily deploy the same model (from any ML library) to batch and real-time scoring on platforms such as Docker, Apache Spark, Azure ML and AWS SageMaker. * `MLflow Model Registry `_: A centralized model store, set of APIs, and UI, to collaboratively manage the full lifecycle of MLflow Models.

TT-NN is a python & C++ Neural Network OP library. It provides a low-level programming model, TT-Metalium, enabling kernel development for Tenstorrent hardware.

Burn is a new comprehensive dynamic Deep Learning Framework built using Rust with extreme flexibility, compute efficiency and portability as its primary goals.

Grand Challenge is a platform that provides access to large amounts of annotated training data, objective comparisons of state-of-the-art machine learning solutions, and clinical validation using real-world data. It assists researchers, data scientists, and clinicians in collaborating to develop robust machine learning solutions to problems in biomedical imaging.

This tool is designed to detect and classify Alzheimer's Disease using Deep Learning and Machine Learning algorithms on an early basis, which is further optimized using the Crow Search Algorithm (CSA). Alzheimer's is a fatal disease, and early detection is crucial for patients to predetermine their condition and prevent its progression. By analyzing MRI scanned images using Artificial Intelligence technology, this tool can classify patients who may or may not develop AD in the future. The CSA algorithm, combined with ML algorithms, has proven to be the most effective approach for this purpose.

OpenCRISPR is a set of free and open gene editing systems designed by Profluent Bio. The OpenCRISPR-1 protein maintains the prototypical architecture of a Type II Cas9 nuclease but is hundreds of mutations away from SpCas9 or any other known natural CRISPR-associated protein. You can view OpenCRISPR-1 as a drop-in replacement for many protocols that need a cas9-like protein with an NGG PAM and you can even use it with canonical SpCas9 gRNAs. OpenCRISPR-1 can be fused in a deactivated or nickase format for next generation gene editing techniques like base, prime, or epigenome editing.

AlphaFold3 is an implementation of the Alpha Fold 3 model in PyTorch for accurate structure prediction of biomolecular interactions. It includes modules for genetic diffusion and full model examples for forward pass computations. The tool allows users to generate random pair and single representations, operate on atomic coordinates, and perform structure predictions based on input tensors. The implementation also provides functionalities for training and evaluating the model.

FuseMedML is a Python framework designed to accelerate machine learning-based discovery in the medical field by promoting code reuse. It provides a flexible design concept where data is stored in a nested dictionary, allowing easy handling of multi-modality information. The framework includes components for creating custom models, loss functions, metrics, and data processing operators. Additionally, FuseMedML offers 'batteries included' key components such as fuse.data for data processing, fuse.eval for model evaluation, and fuse.dl for reusable deep learning components. It supports PyTorch and PyTorch Lightning libraries and encourages the creation of domain extensions for specific medical domains.

The Microsoft Health Intelligence Machine Learning Toolbox is a repository that provides low-level and high-level building blocks for Machine Learning / AI researchers and practitioners. It simplifies and streamlines work on deep learning models for healthcare and life sciences by offering tested components such as data loaders, pre-processing tools, deep learning models, and cloud integration utilities. The repository includes two Python packages, 'hi-ml-azure' for helper functions in AzureML, 'hi-ml' for ML components, and 'hi-ml-cpath' for models and workflows related to histopathology images.

TotalSegmentator is a 3D Slicer extension designed for fully automatic whole body CT segmentation using the 'TotalSegmentator' AI model. The computation time is less than one minute, making it efficient for research purposes. Users can set up GPU acceleration for faster segmentation. The tool provides a user-friendly interface for loading CT images, creating segmentations, and displaying results in 3D. Troubleshooting steps are available for common issues such as failed computation, GPU errors, and inaccurate segmentations. Contributions to the extension are welcome, following 3D Slicer contribution guidelines.

MD-Agent is a LLM-agent based toolset for Molecular Dynamics. It uses Langchain and a collection of tools to set up and execute molecular dynamics simulations, particularly in OpenMM. The tool assists in environment setup, installation, and usage by providing detailed steps. It also requires API keys for certain functionalities, such as OpenAI and paper-qa for literature searches. Contributions to the project are welcome, with a detailed Contributor's Guide available for interested individuals.