
cyclops
A toolkit for evaluating and monitoring AI models in clinical settings
Stars: 79

Cyclops is a toolkit for facilitating research and deployment of ML models for healthcare. It provides a few high-level APIs namely: data - Create datasets for training, inference and evaluation. We use the popular π€ datasets to efficiently load and slice different modalities of data models - Use common model implementations using scikit-learn and PyTorch tasks - Use common ML task formulations such as binary classification or multi-label classification on tabular, time-series and image data evaluate - Evaluate models on clinical prediction tasks monitor - Detect dataset shift relevant for clinical use cases report - Create model report cards for clinical ML models
README:
cyclops
is a toolkit for facilitating research and deployment of ML models for healthcare. It provides a few high-level APIs namely:
-
data
- Create datasets for training, inference and evaluation. We use the popular π€ datasets to efficiently load and slice different modalities of data -
models
- Use common model implementations using scikit-learn and PyTorch -
tasks
- Use common ML task formulations such as binary classification or multi-label classification on tabular, time-series and image data -
evaluate
- Evaluate models on clinical prediction tasks -
monitor
- Detect dataset shift relevant for clinical use cases -
report
- Create model report cards for clinical ML models
cyclops
also provides example end-to-end use case implementations on clinical datasets such as
python3 -m pip install pycyclops
cyclops
has many optional dependencies that are used for specific functionality. For
example, the monai library is used for loading
DICOM images to create datasets. Hence, monai
can be installed using
python3 -m pip install pycyclops[monai]
. Specific sets of dependencies are listed
below.
Dependency | pip extra | Notes |
---|---|---|
xgboost | xgboost | Allows use of XGBoost model |
torch | torch | Allows use of PyTorch models |
torchvision | torchvision | Allows use of Torchvision library |
torchxrayvision | torchxrayvision | Uses TorchXRayVision library |
monai | monai | Uses MONAI to load and transform images |
alibi | alibi | Uses Alibi for additional explainability functionality |
alibi-detect | alibi-detect | Uses Alibi Detect for dataset shift detection |
The development environment can be set up using poetry. Hence, make sure it is installed and then run:
python3 -m poetry install
source $(poetry env info --path)/bin/activate
In order to install dependencies for testing (codestyle, unit tests, integration tests), run:
python3 -m poetry install --with test
API documentation is built using Sphinx and can be locally built by:
python3 -m poetry install --with docs
cd docs
make html SPHINXOPTS="-D nbsphinx_allow_errors=True"
Contributing to cyclops is welcomed. See Contributing for guidelines.
π Documentation
If you need to build the documentations locally, make sure to install Pandoc
in addition to docs
poetry group.
To use jupyter notebooks, the python virtual environment can be installed and used inside an IPython kernel. After activating the virtual environment, run:
python3 -m ipykernel install --user --name <name_of_kernel>
Now, you can navigate to the notebook's Kernel
tab and set it as
<name_of_kernel>
.
Reference to cite when you use cyclops
in a project or a research paper:
@article {Krishnan2022.12.02.22283021,
author = {Krishnan, Amrit and Subasri, Vallijah and McKeen, Kaden and Kore, Ali and Ogidi, Franklin and Alinoori, Mahshid and Lalani, Nadim and Dhalla, Azra and Verma, Amol and Razak, Fahad and Pandya, Deval and Dolatabadi, Elham},
title = {CyclOps: Cyclical development towards operationalizing ML models for health},
elocation-id = {2022.12.02.22283021},
year = {2022},
doi = {10.1101/2022.12.02.22283021},
publisher = {Cold Spring Harbor Laboratory Press},
URL = {https://www.medrxiv.org/content/early/2022/12/08/2022.12.02.22283021},
journal = {medRxiv}
}
For Tasks:
Click tags to check more tools for each tasksFor Jobs:
Alternative AI tools for cyclops
Similar Open Source Tools

cyclops
Cyclops is a toolkit for facilitating research and deployment of ML models for healthcare. It provides a few high-level APIs namely: data - Create datasets for training, inference and evaluation. We use the popular π€ datasets to efficiently load and slice different modalities of data models - Use common model implementations using scikit-learn and PyTorch tasks - Use common ML task formulations such as binary classification or multi-label classification on tabular, time-series and image data evaluate - Evaluate models on clinical prediction tasks monitor - Detect dataset shift relevant for clinical use cases report - Create model report cards for clinical ML models

Qwen
Qwen is a series of large language models developed by Alibaba DAMO Academy. It outperforms the baseline models of similar model sizes on a series of benchmark datasets, e.g., MMLU, C-Eval, GSM8K, MATH, HumanEval, MBPP, BBH, etc., which evaluate the modelsβ capabilities on natural language understanding, mathematic problem solving, coding, etc. Qwen models outperform the baseline models of similar model sizes on a series of benchmark datasets, e.g., MMLU, C-Eval, GSM8K, MATH, HumanEval, MBPP, BBH, etc., which evaluate the modelsβ capabilities on natural language understanding, mathematic problem solving, coding, etc. Qwen-72B achieves better performance than LLaMA2-70B on all tasks and outperforms GPT-3.5 on 7 out of 10 tasks.

Consistency_LLM
Consistency Large Language Models (CLLMs) is a family of efficient parallel decoders that reduce inference latency by efficiently decoding multiple tokens in parallel. The models are trained to perform efficient Jacobi decoding, mapping any randomly initialized token sequence to the same result as auto-regressive decoding in as few steps as possible. CLLMs have shown significant improvements in generation speed on various tasks, achieving up to 3.4 times faster generation. The tool provides a seamless integration with other techniques for efficient Large Language Model (LLM) inference, without the need for draft models or architectural modifications.

notte
Notte is a web browser designed specifically for LLM agents, providing a language-first web navigation experience without the need for DOM/HTML parsing. It transforms websites into structured, navigable maps described in natural language, enabling users to interact with the web using natural language commands. By simplifying browser complexity, Notte allows LLM policies to focus on conversational reasoning and planning, reducing token usage, costs, and latency. The tool supports various language model providers and offers a reinforcement learning style action space and controls for full navigation control.

FlexFlow
FlexFlow Serve is an open-source compiler and distributed system for **low latency**, **high performance** LLM serving. FlexFlow Serve outperforms existing systems by 1.3-2.0x for single-node, multi-GPU inference and by 1.4-2.4x for multi-node, multi-GPU inference.

mLoRA
mLoRA (Multi-LoRA Fine-Tune) is an open-source framework for efficient fine-tuning of multiple Large Language Models (LLMs) using LoRA and its variants. It allows concurrent fine-tuning of multiple LoRA adapters with a shared base model, efficient pipeline parallelism algorithm, support for various LoRA variant algorithms, and reinforcement learning preference alignment algorithms. mLoRA helps save computational and memory resources when training multiple adapters simultaneously, achieving high performance on consumer hardware.

evalverse
Evalverse is an open-source project designed to support Large Language Model (LLM) evaluation needs. It provides a standardized and user-friendly solution for processing and managing LLM evaluations, catering to AI research engineers and scientists. Evalverse supports various evaluation methods, insightful reports, and no-code evaluation processes. Users can access unified evaluation with submodules, request evaluations without code via Slack bot, and obtain comprehensive reports with scores, rankings, and visuals. The tool allows for easy comparison of scores across different models and swift addition of new evaluation tools.

thinc
Thinc is a lightweight deep learning library that offers an elegant, type-checked, functional-programming API for composing models, with support for layers defined in other frameworks such as PyTorch, TensorFlow and MXNet. You can use Thinc as an interface layer, a standalone toolkit or a flexible way to develop new models.

qlib
Qlib is an open-source, AI-oriented quantitative investment platform that supports diverse machine learning modeling paradigms, including supervised learning, market dynamics modeling, and reinforcement learning. It covers the entire chain of quantitative investment, from alpha seeking to order execution. The platform empowers researchers to explore ideas and implement productions using AI technologies in quantitative investment. Qlib collaboratively solves key challenges in quantitative investment by releasing state-of-the-art research works in various paradigms. It provides a full ML pipeline for data processing, model training, and back-testing, enabling users to perform tasks such as forecasting market patterns, adapting to market dynamics, and modeling continuous investment decisions.

weblinx
WebLINX is a Python library and dataset for real-world website navigation with multi-turn dialogue. The repository provides code for training models reported in the WebLINX paper, along with a comprehensive API to work with the dataset. It includes modules for data processing, model evaluation, and utility functions. The modeling directory contains code for processing, training, and evaluating models such as DMR, LLaMA, MindAct, Pix2Act, and Flan-T5. Users can install specific dependencies for HTML processing, video processing, model evaluation, and library development. The evaluation module provides metrics and functions for evaluating models, with ongoing work to improve documentation and functionality.

ABQ-LLM
ABQ-LLM is a novel arbitrary bit quantization scheme that achieves excellent performance under various quantization settings while enabling efficient arbitrary bit computation at the inference level. The algorithm supports precise weight-only quantization and weight-activation quantization. It provides pre-trained model weights and a set of out-of-the-box quantization operators for arbitrary bit model inference in modern architectures.

yolo-flutter-app
Ultralytics YOLO for Flutter is a Flutter plugin that allows you to integrate Ultralytics YOLO computer vision models into your mobile apps. It supports both Android and iOS platforms, providing APIs for object detection and image classification. The plugin leverages Flutter Platform Channels for seamless communication between the client and host, handling all processing natively. Before using the plugin, you need to export the required models in `.tflite` and `.mlmodel` formats. The plugin provides support for tasks like detection and classification, with specific instructions for Android and iOS platforms. It also includes features like camera preview and methods for object detection and image classification on images. Ultralytics YOLO thrives on community collaboration and offers different licensing paths for open-source and commercial use cases.

rag
RAG with txtai is a Retrieval Augmented Generation (RAG) Streamlit application that helps generate factually correct content by limiting the context in which a Large Language Model (LLM) can generate answers. It supports two categories of RAG: Vector RAG, where context is supplied via a vector search query, and Graph RAG, where context is supplied via a graph path traversal query. The application allows users to run queries, add data to the index, and configure various parameters to control its behavior.

AQLM
AQLM is the official PyTorch implementation for Extreme Compression of Large Language Models via Additive Quantization. It includes prequantized AQLM models without PV-Tuning and PV-Tuned models for LLaMA, Mistral, and Mixtral families. The repository provides inference examples, model details, and quantization setups. Users can run prequantized models using Google Colab examples, work with different model families, and install the necessary inference library. The repository also offers detailed instructions for quantization, fine-tuning, and model evaluation. AQLM quantization involves calibrating models for compression, and users can improve model accuracy through finetuning. Additionally, the repository includes information on preparing models for inference and contributing guidelines.

fiftyone-brain
FiftyOne Brain contains the open source AI/ML capabilities for the FiftyOne ecosystem, enabling users to automatically analyze and manipulate their datasets and models. Features include visual similarity search, query by text, finding unique and representative samples, finding media quality problems and annotation mistakes, and more.
For similar tasks

cyclops
Cyclops is a toolkit for facilitating research and deployment of ML models for healthcare. It provides a few high-level APIs namely: data - Create datasets for training, inference and evaluation. We use the popular π€ datasets to efficiently load and slice different modalities of data models - Use common model implementations using scikit-learn and PyTorch tasks - Use common ML task formulations such as binary classification or multi-label classification on tabular, time-series and image data evaluate - Evaluate models on clinical prediction tasks monitor - Detect dataset shift relevant for clinical use cases report - Create model report cards for clinical ML models

gaussian-painters
This tool is a fork of the 3D Gaussian Splatting code. It allows users to create a dataset ready to be trained with the Gaussian Splatting code. The dataset can be used for various experiments, such as creating orthogonal images, steganography, and lenticular effects. The tool also includes a visualizer that allows users to visualize the "painting" process during the Gaussian Splatting optimization.

UHGEval
UHGEval is a comprehensive framework designed for evaluating the hallucination phenomena. It includes UHGEval, a framework for evaluating hallucination, XinhuaHallucinations dataset, and UHGEval-dataset pipeline for creating XinhuaHallucinations. The framework offers flexibility and extensibility for evaluating common hallucination tasks, supporting various models and datasets. Researchers can use the open-source pipeline to create customized datasets. Supported tasks include QA, dialogue, summarization, and multi-choice tasks.

RAGFoundry
RAG Foundry is a library designed to enhance Large Language Models (LLMs) by fine-tuning models on RAG-augmented datasets. It helps create training data, train models using parameter-efficient finetuning (PEFT), and measure performance using RAG-specific metrics. The library is modular, customizable using configuration files, and facilitates prototyping with various RAG settings and configurations for tasks like data processing, retrieval, training, inference, and evaluation.

ollama-ebook-summary
The 'ollama-ebook-summary' repository is a Python project that creates bulleted notes summaries of books and long texts, particularly in epub and pdf formats with ToC metadata. It automates the extraction of chapters, splits them into ~2000 token chunks, and allows for asking arbitrary questions to parts of the text for improved granularity of response. The tool aims to provide summaries for each page of a book rather than a one-page summary of the entire document, enhancing content curation and knowledge sharing capabilities.

agentneo
AgentNeo is a Python package that provides functionalities for project, trace, dataset, experiment management. It allows users to authenticate, create projects, trace agents and LangGraph graphs, manage datasets, and run experiments with metrics. The tool aims to streamline AI project management and analysis by offering a comprehensive set of features.

RAG-FiT
RAG-FiT is a library designed to improve Language Models' ability to use external information by fine-tuning models on specially created RAG-augmented datasets. The library assists in creating training data, training models using parameter-efficient finetuning (PEFT), and evaluating performance using RAG-specific metrics. It is modular, customizable via configuration files, and facilitates fast prototyping and experimentation with various RAG settings and configurations.

RagaAI-Catalyst
RagaAI Catalyst is a comprehensive platform designed to enhance the management and optimization of LLM projects. It offers features such as project management, dataset management, evaluation management, trace management, prompt management, synthetic data generation, and guardrail management. These functionalities enable efficient evaluation and safeguarding of LLM applications.
For similar jobs

cyclops
Cyclops is a toolkit for facilitating research and deployment of ML models for healthcare. It provides a few high-level APIs namely: data - Create datasets for training, inference and evaluation. We use the popular π€ datasets to efficiently load and slice different modalities of data models - Use common model implementations using scikit-learn and PyTorch tasks - Use common ML task formulations such as binary classification or multi-label classification on tabular, time-series and image data evaluate - Evaluate models on clinical prediction tasks monitor - Detect dataset shift relevant for clinical use cases report - Create model report cards for clinical ML models

weave
Weave is a toolkit for developing Generative AI applications, built by Weights & Biases. With Weave, you can log and debug language model inputs, outputs, and traces; build rigorous, apples-to-apples evaluations for language model use cases; and organize all the information generated across the LLM workflow, from experimentation to evaluations to production. Weave aims to bring rigor, best-practices, and composability to the inherently experimental process of developing Generative AI software, without introducing cognitive overhead.

agentcloud
AgentCloud is an open-source platform that enables companies to build and deploy private LLM chat apps, empowering teams to securely interact with their data. It comprises three main components: Agent Backend, Webapp, and Vector Proxy. To run this project locally, clone the repository, install Docker, and start the services. The project is licensed under the GNU Affero General Public License, version 3 only. Contributions and feedback are welcome from the community.

oss-fuzz-gen
This framework generates fuzz targets for real-world `C`/`C++` projects with various Large Language Models (LLM) and benchmarks them via the `OSS-Fuzz` platform. It manages to successfully leverage LLMs to generate valid fuzz targets (which generate non-zero coverage increase) for 160 C/C++ projects. The maximum line coverage increase is 29% from the existing human-written targets.

LLMStack
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.

VisionCraft
The VisionCraft API is a free API for using over 100 different AI models. From images to sound.

kaito
Kaito is an operator that automates the AI/ML inference model deployment in a Kubernetes cluster. It manages large model files using container images, avoids tuning deployment parameters to fit GPU hardware by providing preset configurations, auto-provisions GPU nodes based on model requirements, and hosts large model images in the public Microsoft Container Registry (MCR) if the license allows. Using Kaito, the workflow of onboarding large AI inference models in Kubernetes is largely simplified.

PyRIT
PyRIT is an open access automation framework designed to empower security professionals and ML engineers to red team foundation models and their applications. It automates AI Red Teaming tasks to allow operators to focus on more complicated and time-consuming tasks and can also identify security harms such as misuse (e.g., malware generation, jailbreaking), and privacy harms (e.g., identity theft). The goal is to allow researchers to have a baseline of how well their model and entire inference pipeline is doing against different harm categories and to be able to compare that baseline to future iterations of their model. This allows them to have empirical data on how well their model is doing today, and detect any degradation of performance based on future improvements.