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.
aihwkit
The IBM Analog Hardware Acceleration Kit is an open-source Python toolkit for exploring and using the capabilities of in-memory computing devices in the context of artificial intelligence. It consists of two main components: Pytorch integration and Analog devices simulator. The Pytorch integration provides a series of primitives and features that allow using the toolkit within PyTorch, including analog neural network modules, analog training using torch training workflow, and analog inference using torch inference workflow. The Analog devices simulator is a high-performant (CUDA-capable) C++ simulator that allows for simulating a wide range of analog devices and crossbar configurations by using abstract functional models of material characteristics with adjustable parameters. Along with the two main components, the toolkit includes other functionalities such as a library of device presets, a module for executing high-level use cases, a utility to automatically convert a downloaded model to its equivalent Analog model, and integration with the AIHW Composer platform. The toolkit is currently in beta and under active development, and users are advised to be mindful of potential issues and keep an eye for improvements, new features, and bug fixes in upcoming versions.
hallucination-index
LLM Hallucination Index - RAG Special is a comprehensive evaluation of large language models (LLMs) focusing on context length and open vs. closed-source attributes. The index explores the impact of context length on model performance and tests the assumption that closed-source LLMs outperform open-source ones. It also investigates the effectiveness of prompting techniques like Chain-of-Note across different context lengths. The evaluation includes 22 models from various brands, analyzing major trends and declaring overall winners based on short, medium, and long context insights. Methodologies involve rigorous testing with different context lengths and prompting techniques to assess models' abilities in handling extensive texts and detecting hallucinations.
Nanoflow
NanoFlow is a throughput-oriented high-performance serving framework for Large Language Models (LLMs) that consistently delivers superior throughput compared to other frameworks by utilizing key techniques such as intra-device parallelism, asynchronous CPU scheduling, and SSD offloading. The framework proposes nano-batching to schedule compute-, memory-, and network-bound operations for simultaneous execution, leading to increased resource utilization. NanoFlow also adopts an asynchronous control flow to optimize CPU overhead and eagerly offloads KV-Cache to SSDs for multi-round conversations. The open-source codebase integrates state-of-the-art kernel libraries and provides necessary scripts for environment setup and experiment reproduction.
SuperKnowa
SuperKnowa is a fast framework to build Enterprise RAG (Retriever Augmented Generation) Pipelines at Scale, powered by watsonx. It accelerates Enterprise Generative AI applications to get prod-ready solutions quickly on private data. The framework provides pluggable components for tackling various Generative AI use cases using Large Language Models (LLMs), allowing users to assemble building blocks to address challenges in AI-driven text generation. SuperKnowa is battle-tested from 1M to 200M private knowledge base & scaled to billions of retriever tokens.
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.
End-to-End-LLM
The End-to-End LLM Bootcamp is a comprehensive training program that covers the entire process of developing and deploying large language models. Participants learn to preprocess datasets, train models, optimize performance using NVIDIA technologies, understand guardrail prompts, and deploy AI pipelines using Triton Inference Server. The bootcamp includes labs, challenges, and practical applications, with a total duration of approximately 7.5 hours. It is designed for individuals interested in working with advanced language models and AI technologies.
awesome-transformer-nlp
This repository contains a hand-curated list of great machine (deep) learning resources for Natural Language Processing (NLP) with a focus on Generative Pre-trained Transformer (GPT), Bidirectional Encoder Representations from Transformers (BERT), attention mechanism, Transformer architectures/networks, Chatbot, and transfer learning in NLP.
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.
AlphaFold3
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.
param
PARAM Benchmarks is a repository of communication and compute micro-benchmarks as well as full workloads for evaluating training and inference platforms. It complements commonly used benchmarks by focusing on AI training with PyTorch based collective benchmarks, GEMM, embedding lookup, linear layer, and DLRM communication patterns. The tool bridges the gap between stand-alone C++ benchmarks and PyTorch/Tensorflow based application benchmarks, providing deep insights into system architecture and framework-level overheads.
openspg
OpenSPG is a knowledge graph engine developed by Ant Group in collaboration with OpenKG, based on the SPG (Semantic-enhanced Programmable Graph) framework. It provides explicit semantic representations, logical rule definitions, operator frameworks (construction, inference), and other capabilities for domain knowledge graphs. OpenSPG supports pluggable adaptation of basic engines and algorithmic services by various vendors to build customized solutions.
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.
llm-hosting-container
The LLM Hosting Container repository provides Dockerfile and associated resources for building and hosting containers for large language models, specifically the HuggingFace Text Generation Inference (TGI) container. This tool allows users to easily deploy and manage large language models in a containerized environment, enabling efficient inference and deployment of language-based applications.
AI.Labs
AI.Labs is an open-source project that integrates advanced artificial intelligence technologies to create a powerful AI platform. It focuses on integrating AI services like large language models, speech recognition, and speech synthesis for functionalities such as dialogue, voice interaction, and meeting transcription. The project also includes features like a large language model dialogue system, speech recognition for meeting transcription, speech-to-text voice synthesis, integration of translation and chat, and uses technologies like C#, .Net, SQLite database, XAF, OpenAI API, TTS, and STT.
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.
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.