cellseg_models.pytorch

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.

Apollo is a multilingual medical LLM that covers English, Chinese, French, Hindi, Spanish, Hindi, and Arabic. It is designed to democratize medical AI to 6B people. Apollo has achieved state-of-the-art results on a variety of medical NLP tasks, including question answering, medical dialogue generation, and medical text classification. Apollo is easy to use and can be integrated into a variety of applications, making it a valuable tool for healthcare professionals and researchers.

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.

genai is a multi-AI providers library for Rust that aims to provide a common and ergonomic single API to various generative AI providers such as OpenAI, Anthropic, Cohere, Ollama, and Gemini. It focuses on standardizing chat completion APIs across major AI services, prioritizing ergonomics and commonality. The library initially focuses on text chat APIs and plans to expand to support images, function calling, and more in the future versions. Version 0.1.x will have breaking changes in patches, while version 0.2.x will follow semver more strictly. genai does not provide a full representation of a given AI provider but aims to simplify the differences at a lower layer for ease of use.

Easy, fast, and cheap pretrain, finetune, serving for everyone

SGLang is a structured generation language designed for large language models (LLMs). It makes your interaction with LLMs faster and more controllable by co-designing the frontend language and the runtime system. The core features of SGLang include: - **A Flexible Front-End Language**: This allows for easy programming of LLM applications with multiple chained generation calls, advanced prompting techniques, control flow, multiple modalities, parallelism, and external interaction. - **A High-Performance Runtime with RadixAttention**: This feature significantly accelerates the execution of complex LLM programs by automatic KV cache reuse across multiple calls. It also supports other common techniques like continuous batching and tensor parallelism.

Funcchain is a Python library that allows you to easily write cognitive systems by leveraging Pydantic models as output schemas and LangChain in the backend. It provides a seamless integration of LLMs into your apps, utilizing OpenAI Functions or LlamaCpp grammars (json-schema-mode) for efficient structured output. Funcchain compiles the Funcchain syntax into LangChain runnables, enabling you to invoke, stream, or batch process your pipelines effortlessly.

The Beta Machine Learning Toolkit is a package containing various algorithms and utilities for implementing machine learning workflows in multiple languages, including Julia, Python, and R. It offers a range of supervised and unsupervised models, data transformers, and assessment tools. The models are implemented entirely in Julia and are not wrappers for third-party models. Users can easily contribute new models or request implementations. The focus is on user-friendliness rather than computational efficiency, making it suitable for educational and research purposes.

LLMLight is a novel framework that employs Large Language Models (LLMs) as decision-making agents for Traffic Signal Control (TSC). The framework leverages the advanced generalization capabilities of LLMs to engage in a reasoning and decision-making process akin to human intuition for effective traffic control. LLMLight has been demonstrated to be remarkably effective, generalizable, and interpretable against various transportation-based and RL-based baselines on nine real-world and synthetic datasets.

Educhain is a powerful Python package that leverages Generative AI to create engaging and personalized educational content. It enables users to generate multiple-choice questions, create lesson plans, and support various LLM models. Users can export questions to JSON, PDF, and CSV formats, customize prompt templates, and generate questions from text, PDF, URL files, youtube videos, and images. Educhain outperforms traditional methods in content generation speed and quality. It offers advanced configuration options and has a roadmap for future enhancements, including integration with popular Learning Management Systems and a mobile app for content generation on-the-go.

AI00 RWKV Server is an inference API server for the RWKV language model based upon the web-rwkv inference engine. It supports VULKAN parallel and concurrent batched inference and can run on all GPUs that support VULKAN. No need for Nvidia cards!!! AMD cards and even integrated graphics can be accelerated!!! No need for bulky pytorch, CUDA and other runtime environments, it's compact and ready to use out of the box! Compatible with OpenAI's ChatGPT API interface. 100% open source and commercially usable, under the MIT license. If you are looking for a fast, efficient, and easy-to-use LLM API server, then AI00 RWKV Server is your best choice. It can be used for various tasks, including chatbots, text generation, translation, and Q&A.

AnglE is a library for training state-of-the-art BERT/LLM-based sentence embeddings with just a few lines of code. It also serves as a general sentence embedding inference framework, allowing for inferring a variety of transformer-based sentence embeddings. The library supports various loss functions such as AnglE loss, Contrastive loss, CoSENT loss, and Espresso loss. It provides backbones like BERT-based models, LLM-based models, and Bi-directional LLM-based models for training on single or multi-GPU setups. AnglE has achieved significant performance on various benchmarks and offers official pretrained models for both BERT-based and LLM-based models.

GPTQModel is an easy-to-use LLM quantization and inference toolkit based on the GPTQ algorithm. It provides support for weight-only quantization and offers features such as dynamic per layer/module flexible quantization, sharding support, and auto-heal quantization errors. The toolkit aims to ensure inference compatibility with HF Transformers, vLLM, and SGLang. It offers various model supports, faster quant inference, better quality quants, and security features like hash check of model weights. GPTQModel also focuses on faster quantization, improved quant quality as measured by PPL, and backports bug fixes from AutoGPTQ.

Open-Lyrics is a Python library that transcribes voice files using faster-whisper and translates/polishes the resulting text into `.lrc` files in the desired language using LLM, e.g. OpenAI-GPT, Anthropic-Claude. It offers well preprocessed audio to reduce hallucination and context-aware translation to improve translation quality. Users can install the library from PyPI or GitHub and follow the installation steps to set up the environment. The tool supports GUI usage and provides Python code examples for transcription and translation tasks. It also includes features like utilizing context and glossary for translation enhancement, pricing information for different models, and a list of todo tasks for future improvements.

Ax is a Typescript library that allows users to build intelligent agents inspired by agentic workflows and the Stanford DSP paper. It seamlessly integrates with multiple Large Language Models (LLMs) and VectorDBs to create RAG pipelines or collaborative agents capable of solving complex problems. The library offers advanced features such as streaming validation, multi-modal DSP, and automatic prompt tuning using optimizers. Users can easily convert documents of any format to text, perform smart chunking, embedding, and querying, and ensure output validation while streaming. Ax is production-ready, written in Typescript, and has zero dependencies.

E2M is a Python library that can parse and convert various file types into Markdown format. It supports the conversion of multiple file formats, including doc, docx, epub, html, htm, url, pdf, ppt, pptx, mp3, and m4a. The ultimate goal of the E2M project is to provide high-quality data for Retrieval-Augmented Generation (RAG) and model training or fine-tuning. The core architecture consists of a Parser responsible for parsing various file types into text or image data, and a Converter responsible for converting text or image data into Markdown format.

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.

PyLLMs is a minimal Python library designed to connect to various Language Model Models (LLMs) such as OpenAI, Anthropic, Google, AI21, Cohere, Aleph Alpha, and HuggingfaceHub. It provides a built-in model performance benchmark for fast prototyping and evaluating different models. Users can easily connect to top LLMs, get completions from multiple models simultaneously, and evaluate models on quality, speed, and cost. The library supports asynchronous completion, streaming from compatible models, and multi-model initialization for testing and comparison. Additionally, it offers features like passing chat history, system messages, counting tokens, and benchmarking models based on quality, speed, and cost.

A fine-tuning guide for both OpenAI and Open-Source Large Language Models on Azure. Fine-Tuning retrains an existing pre-trained LLM using example data, resulting in a new 'custom' fine-tuned LLM optimized for task-specific examples. Use cases include improving LLM performance on specific tasks and introducing information not well represented by the base LLM model. Suitable for cases where latency is critical, high accuracy is required, and clear evaluation metrics are available. Learning path includes labs for fine-tuning GPT and Llama2 models via Dashboards and Python SDK.

Awesome Mobile LLMs is a curated list of Large Language Models (LLMs) and related studies focused on mobile and embedded hardware. The repository includes information on various LLM models, deployment frameworks, benchmarking efforts, applications, multimodal LLMs, surveys on efficient LLMs, training LLMs on device, mobile-related use-cases, industry announcements, and related repositories. It aims to be a valuable resource for researchers, engineers, and practitioners interested in mobile LLMs.

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.

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.

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.