aitom
AI for tomography
Stars: 131
AITom is an open-source platform for AI-driven cellular electron cryo-tomography analysis. It is developed to process large amounts of Cryo-ET data, reconstruct, detect, classify, recover, and spatially model different cellular components using state-of-the-art machine learning approaches. The platform aims to automate cellular structure discovery and provide new insights into molecular biology and medical applications.
README:
AITom is an open-source platform for AI driven cellular electron cryo-tomography analysis.
AITom is originated from the tomominer library, adapted from an extended version of the tomominer library, developed at Alber Lab.
Code and data for projects developed and maintained by Xu Lab and collaborators.
The research related to the code and data can be found at http://cs.cmu.edu/~mxu1
Nearly every major process in a cell is orchestrated by the interplay of macromolecular assemblies, which often coordinate their actions as functional modules in biochemical pathways. To proceed efficiently, this interplay between different macromolecular machines often requires a distinctly nonrandom spatial organization in the cell. With the recent revolutions in cellular Cryo-Electron Tomography (Cryo-ET) imaging technologies, it is now possible to generate 3D reconstructions of cells in hydrated, close to native states at submolecular resolution.
We are developing computational analysis techniques for processing large amounts of Cryo-ET data to reconstruct, detect, classify, recover, and spatially model different cellular components. We utilize state-of-the-art machine learning (including deep learning) approaches to design Cryo-ET specific data analysis and modeling algorithms. Our research automates the cellular structure discovery and will lead to new insights into the basic molecular biology and medical applications.
De novo structural mining pipeline results: (a). A slice of a rat neuron tomogram, (b). Recovered patterns (from left to right): mitochondrial membrane, Ribosome-like pattern, ellipsoid of strong signals, TRiC-like pattern, borders of ice crystal, (c). Pattern mining results embedded, (d). Individual patterns embedded.
Technical report: AITom: Open-source AI platform for cryo-electron Tomography data analysis
@article{zeng2019aitom,
title={AITom: Open-source AI platform for cryo-electron Tomography data analysis},
author={Zeng, Xiangrui and Xu, Min},
journal={arXiv preprint arXiv:1911.03044},
year={2019}
}
For Tasks:
Click tags to check more tools for each tasksFor Jobs:
Alternative AI tools for aitom
Similar Open Source Tools
aitom
AITom is an open-source platform for AI-driven cellular electron cryo-tomography analysis. It is developed to process large amounts of Cryo-ET data, reconstruct, detect, classify, recover, and spatially model different cellular components using state-of-the-art machine learning approaches. The platform aims to automate cellular structure discovery and provide new insights into molecular biology and medical applications.
matchem-llm
A public repository collecting links to state-of-the-art training sets, QA, benchmarks and other evaluations for various ML and LLM applications in materials science and chemistry. It includes datasets related to chemistry, materials, multimodal data, and knowledge graphs in the field. The repository aims to provide resources for training and evaluating machine learning models in the materials science and chemistry domains.
EScAIP
EScAIP is an Efficiently Scaled Attention Interatomic Potential that leverages a novel multi-head self-attention formulation within graph neural networks to predict energy and forces between atoms in molecules and materials. It achieves substantial gains in efficiency, at least 10x speed up in inference time and 5x less memory usage compared to existing models. EScAIP represents a philosophy towards developing general-purpose Neural Network Interatomic Potentials that achieve better expressivity through scaling and continue to scale efficiently with increased computational resources and training data.
automatic-KG-creation-with-LLM
This repository presents a (semi-)automatic pipeline for Ontology and Knowledge Graph Construction using Large Language Models (LLMs) such as Mixtral 8x22B Instruct v0.1, GPT-4o, GPT-3.5, and Gemini. It explores the generation of Knowledge Graphs by formulating competency questions, developing ontologies, constructing KGs, and evaluating the results with minimal human involvement. The project showcases the creation of a KG on deep learning methodologies from scholarly publications. It includes components for data preprocessing, prompts for LLMs, datasets, and results from the selected LLMs.
awesome-generative-ai-guide
This repository serves as a comprehensive hub for updates on generative AI research, interview materials, notebooks, and more. It includes monthly best GenAI papers list, interview resources, free courses, and code repositories/notebooks for developing generative AI applications. The repository is regularly updated with the latest additions to keep users informed and engaged in the field of generative AI.
Main
This repository contains material related to the new book _Synthetic Data and Generative AI_ by the author, including code for NoGAN, DeepResampling, and NoGAN_Hellinger. NoGAN is a tabular data synthesizer that outperforms GenAI methods in terms of speed and results, utilizing state-of-the-art quality metrics. DeepResampling is a fast NoGAN based on resampling and Bayesian Models with hyperparameter auto-tuning. NoGAN_Hellinger combines NoGAN and DeepResampling with the Hellinger model evaluation metric.
ai-algorithms
This repository is a work in progress that contains first-principle implementations of groundbreaking AI algorithms using various deep learning frameworks. Each implementation is accompanied by supporting research papers, aiming to provide comprehensive educational resources for understanding and implementing foundational AI algorithms from scratch.
grand-challenge.org
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.
ianvs
Ianvs is a distributed synergy AI benchmarking project incubated in KubeEdge SIG AI. It aims to test the performance of distributed synergy AI solutions following recognized standards, providing end-to-end benchmark toolkits, test environment management tools, test case control tools, and benchmark presentation tools. It also collaborates with other organizations to establish comprehensive benchmarks and related applications. The architecture includes critical components like Test Environment Manager, Test Case Controller, Generation Assistant, Simulation Controller, and Story Manager. Ianvs documentation covers quick start, guides, dataset descriptions, algorithms, user interfaces, stories, and roadmap.
WeatherGFT
WeatherGFT is a physics-AI hybrid model designed to generalize weather forecasts to finer-grained temporal scales beyond the training dataset. It incorporates physical partial differential equations (PDEs) into neural networks to simulate fine-grained physical evolution and correct biases. The model achieves state-of-the-art performance in forecasting tasks at different time scales, from nowcasting to medium-range forecasts, by utilizing a lead time-aware training framework and a carefully designed PDE kernel. WeatherGFT bridges the gap between nowcast and medium-range forecast by extending forecasting abilities to predict accurately at a 30-minute time scale.
kaapana
Kaapana is an open-source toolkit for state-of-the-art platform provisioning in the field of medical data analysis. The applications comprise AI-based workflows and federated learning scenarios with a focus on radiological and radiotherapeutic imaging. Obtaining large amounts of medical data necessary for developing and training modern machine learning methods is an extremely challenging effort that often fails in a multi-center setting, e.g. due to technical, organizational and legal hurdles. A federated approach where the data remains under the authority of the individual institutions and is only processed on-site is, in contrast, a promising approach ideally suited to overcome these difficulties. Following this federated concept, the goal of Kaapana is to provide a framework and a set of tools for sharing data processing algorithms, for standardized workflow design and execution as well as for performing distributed method development. This will facilitate data analysis in a compliant way enabling researchers and clinicians to perform large-scale multi-center studies. By adhering to established standards and by adopting widely used open technologies for private cloud development and containerized data processing, Kaapana integrates seamlessly with the existing clinical IT infrastructure, such as the Picture Archiving and Communication System (PACS), and ensures modularity and easy extensibility.
algebraic-nnhw
This repository contains the source code for a GEMM & deep learning hardware accelerator system used to validate proposed systolic array hardware architectures implementing efficient matrix multiplication algorithms to increase performance-per-area limits of GEMM & AI accelerators. Achieved results include up to 3× faster CNN inference, >2× higher mults/multiplier/clock cycle, and low area with high clock frequency. The system is specialized for inference of non-sparse DNN models with fixed-point/quantized inputs, fully accelerating all DNN layers in hardware, and highly optimizing GEMM acceleration.
sharpneat
SharpNEAT is a complete implementation of NEAT written in C# and targeting .NET 9. It provides an implementation of an Evolutionary Algorithm (EA) with the specific goal of evolving a population of neural networks towards solving some goal problem task. The framework facilitates research into evolutionary computation and specifically evolution of neural networks, allowing for modular experimentation with genetic coding and evolutionary algorithms.
LAMBDA
LAMBDA is a code-free multi-agent data analysis system that utilizes large models to address data analysis challenges in complex data-driven applications. It allows users to perform complex data analysis tasks through human language instruction, seamlessly generate and debug code using two key agent roles, integrate external models and algorithms, and automatically generate reports. The system has demonstrated strong performance on various machine learning datasets, enhancing data science practice by integrating human and artificial intelligence.
miles-credit
CREDIT is an open software platform for training and deploying AI atmospheric prediction models. It offers fast models with flexible configuration options for input data and neural network architecture. The user-friendly interface enables quick setup and iteration. Developed by the MILES group and NSF National Center for Atmospheric Research, CREDIT combines advanced AI/ML with atmospheric science expertise. It provides a stable release with various models, training, and deployment options, with ongoing development. Detailed documentation is available for installation, training, deployment, config file interpretation, and API usage.
For similar tasks
aitom
AITom is an open-source platform for AI-driven cellular electron cryo-tomography analysis. It is developed to process large amounts of Cryo-ET data, reconstruct, detect, classify, recover, and spatially model different cellular components using state-of-the-art machine learning approaches. The platform aims to automate cellular structure discovery and provide new insights into molecular biology and medical applications.
gonzo
Gonzo is a powerful, real-time log analysis terminal UI tool inspired by k9s. It allows users to analyze log streams with beautiful charts, AI-powered insights, and advanced filtering directly from the terminal. The tool provides features like live streaming log processing, OTLP support, interactive dashboard with real-time charts, advanced filtering options including regex support, and AI-powered insights such as pattern detection, anomaly analysis, and root cause suggestions. Users can also configure AI models from providers like OpenAI, LM Studio, and Ollama for intelligent log analysis. Gonzo is built with Bubble Tea, Lipgloss, Cobra, Viper, and OpenTelemetry, following a clean architecture with separate modules for TUI, log analysis, frequency tracking, OTLP handling, and AI integration.
angular-node-java-ai
This repository contains a project that integrates Angular frontend, Node.js backend, Java services, and AI capabilities. The project aims to demonstrate a full-stack application with modern technologies and AI features. It showcases how to build a scalable and efficient system using Angular for the frontend, Node.js for the backend, Java for services, and AI for advanced functionalities.
For similar jobs
sweep
Sweep is an AI junior developer that turns bugs and feature requests into code changes. It automatically handles developer experience improvements like adding type hints and improving test coverage.
teams-ai
The Teams AI Library is a software development kit (SDK) that helps developers create bots that can interact with Teams and Microsoft 365 applications. It is built on top of the Bot Framework SDK and simplifies the process of developing bots that interact with Teams' artificial intelligence capabilities. The SDK is available for JavaScript/TypeScript, .NET, and Python.
ai-guide
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.
classifai
Supercharge WordPress Content Workflows and Engagement with Artificial Intelligence. Tap into leading cloud-based services like OpenAI, Microsoft Azure AI, Google Gemini and IBM Watson to augment your WordPress-powered websites. Publish content faster while improving SEO performance and increasing audience engagement. ClassifAI integrates Artificial Intelligence and Machine Learning technologies to lighten your workload and eliminate tedious tasks, giving you more time to create original content that matters.
chatbot-ui
Chatbot UI is an open-source AI chat app that allows users to create and deploy their own AI chatbots. It is easy to use and can be customized to fit any need. Chatbot UI is perfect for businesses, developers, and anyone who wants to create a chatbot.
BricksLLM
BricksLLM is a cloud native AI gateway written in Go. Currently, it provides native support for OpenAI, Anthropic, Azure OpenAI and vLLM. BricksLLM aims to provide enterprise level infrastructure that can power any LLM production use cases. Here are some use cases for BricksLLM: * Set LLM usage limits for users on different pricing tiers * Track LLM usage on a per user and per organization basis * Block or redact requests containing PIIs * Improve LLM reliability with failovers, retries and caching * Distribute API keys with rate limits and cost limits for internal development/production use cases * Distribute API keys with rate limits and cost limits for students
uAgents
uAgents is a Python library developed by Fetch.ai that allows for the creation of autonomous AI agents. These agents can perform various tasks on a schedule or take action on various events. uAgents are easy to create and manage, and they are connected to a fast-growing network of other uAgents. They are also secure, with cryptographically secured messages and wallets.
griptape
Griptape is a modular Python framework for building AI-powered applications that securely connect to your enterprise data and APIs. It offers developers the ability to maintain control and flexibility at every step. Griptape's core components include Structures (Agents, Pipelines, and Workflows), Tasks, Tools, Memory (Conversation Memory, Task Memory, and Meta Memory), Drivers (Prompt and Embedding Drivers, Vector Store Drivers, Image Generation Drivers, Image Query Drivers, SQL Drivers, Web Scraper Drivers, and Conversation Memory Drivers), Engines (Query Engines, Extraction Engines, Summary Engines, Image Generation Engines, and Image Query Engines), and additional components (Rulesets, Loaders, Artifacts, Chunkers, and Tokenizers). Griptape enables developers to create AI-powered applications with ease and efficiency.
