Repository Index

The repository host gives no description.

• foundation-model
• gpt
• single-cell

Biological foundation modeling from molecular to genome scale

TorchXRayVision: A library of chest X-ray datasets and models. Classifiers, segmentation, and autoencoders.

• medical-imaging
• medical-ai
• deep-learning
• machine-learning

This rocq library aims to formalize a substantial body of mathematics using the univalent point of view.

• coq
• mathematics
• unimath
• coq-library

Foundation Models for Genomics & Transcriptomics

• genomics
• deep-learning
• transformer
• dna

Official implementation for HyenaDNA, a long-range genomic foundation model built with Hyena

• foundation-models
• genomics
• language-models

Pathology Foundation Model - Nature Medicine

• foundation
• foundation-model
• histopathology
• mahmoodlab

Clinical Histopathology Imaging Evaluation Foundation Model

Prov-GigaPath: A whole-slide foundation model for digital pathology from real-world data

Vision-Language Pathology Foundation Model - Nature Medicine

• bioimage-analysis
• bioimage-informatics
• conch
• foundation-model

[ICLR 2024] DNABERT-2: Efficient Foundation Model and Benchmark for Multi-Species Genome

• dataset
• dna
• dna-processing
• dna-training

The repository host gives no description.

Pathology Language and Image Pre-Training (PLIP) is the first vision and language foundation model for Pathology AI (Nature Medicine). PLIP is a large-scale pre-trained model that can be used to extract visual and language features from pathology images and text description. The model is a fine-tuned version of the original CLIP model.

• artificial-intelligence
• clip
• pathology
• vision-and-language

UCE is a zero-shot foundation model for single-cell gene expression data

Repository for Nicheformer: a foundation model for single-cell and spatial omics

🏃 The go-to single-cell Foundation Model

• batch-correction
• cell-biology
• celltype-annotation
• denoising

BulkFormer: A large-scale foundation model for human bulk transcriptomes

Repository for paper scMulan: a multitask generative pre-trained language model for single-cell analysis.

• foundation-models
• gpt
• single-cell

A foundation model-driven whole slide image-scale cell phenotyping method with QuPath integration Resources

• bioimage-analysis
• cell-classification
• computer-vision
• digital-pathology

CancerFoundation: A single-cell RNA sequencing foundation model to decipher drug resistance in cancer

• cancer
• foundation-model
• single-cell