Best AI tools for< Tissue Engineer >

Valo is a company that uses AI-driven technology to transform the discovery and development of life-changing medicines. They combine machine learning, tissue biology, and patient data to create a suite of powerful capabilities that bring the future of drug discovery and development to bear. Valo's team of software engineers, data scientists, biologists, medicinal chemists, and big-picture thinkers are dedicated to advancing the combined power of technology and patient data.

Paige is a leading AI company revolutionizing pathology with next-generation technology. They provide diagnostic and biomarker AI, predictive analytics technology, and AI-assisted applications to support cancer detection, subtyping, and molecular biomarker discovery from tissue samples. Paige offers a range of AI suites for prostate, breast, colon, and PanCancer, as well as the innovative Paige Alba™ multi-modal co-pilot. Their advanced AI technology and services help streamline AI development, optimize existing applications, and drive groundbreaking advancements in cancer care.

GRAIL is a healthcare company innovating to solve medicine’s most important challenges. Our team of leading scientists, engineers and clinicians are on an urgent mission to detect cancer early, when it is more treatable and potentially curable. GRAIL's Galleri® test is a first-of-its-kind multi-cancer early detection (MCED) test that can detect a signal shared by more than 50 cancer types and predict the tissue type or organ associated with the signal to help healthcare providers determine next steps.

Trinity is an Explainable AI (XAI) Analysis and Visualization tool designed for Deep Learning systems or other models performing complex classification or decoding. It provides performance analysis through interactive 3D projections that are hyper-dimensional aware, allowing users to explore hyperspace, hypersurface, projections, and manifolds. Trinity primarily works with JSON data formats and supports the visualization of FeatureVector objects. Users can analyze and visualize data points, correlate inputs with classification results, and create custom color maps for better data interpretation. Trinity has been successfully applied to various use cases including Deep Learning Object detection models, COVID gene/tissue classification, Brain Computer Interface decoders, and Large Language Model (ChatGPT) Embeddings Analysis.

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.

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.

SurveyX is an advanced academic survey automation system that leverages Large Language Models (LLMs) to generate high-quality, domain-specific academic papers and surveys. Users can request comprehensive academic papers or surveys tailored to specific topics by providing a paper title and keywords for literature retrieval. The system streamlines academic research by automating paper creation, saving users time and effort in compiling research content.

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.

The RISE Journal Club is a bi-weekly reading group that provides a friendly environment for discussing state-of-the-art papers in medical image analysis, AI, and computer vision. The club aims to enhance critical and design thinking skills essential for researchers. Moderators introduce papers for discussion on various topics such as registration, segmentation, federated learning, fairness, and reinforcement learning. The club covers papers from machine and deep learning communities, offering a broad overview of cutting-edge methods.

AITemplate (AIT) is a Python framework that transforms deep neural networks into CUDA (NVIDIA GPU) / HIP (AMD GPU) C++ code for lightning-fast inference serving. It offers high performance close to roofline fp16 TensorCore (NVIDIA GPU) / MatrixCore (AMD GPU) performance on major models. AITemplate is unified, open, and flexible, supporting a comprehensive range of fusions for both GPU platforms. It provides excellent backward capability, horizontal fusion, vertical fusion, memory fusion, and works with or without PyTorch. FX2AIT is a tool that converts PyTorch models into AIT for fast inference serving, offering easy conversion and expanded support for models with unsupported operators.

MOOSE 2.0 is a leaner, meaner, and stronger tool for 3D medical image segmentation. It is built on the principles of data-centric AI and offers a wide range of segmentation models for both clinical and preclinical settings. MOOSE 2.0 is also versatile, allowing users to use it as a command-line tool for batch processing or as a library package for individual processing in Python projects. With its improved speed, accuracy, and flexibility, MOOSE 2.0 is the go-to tool for segmentation tasks.

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.

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