WangLab @ U of T (@bowang-lab)
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Top repositories

1

MedSAM

Segment Anything in Medical Images
Jupyter Notebook
2,848
star
2

scGPT

Jupyter Notebook
1,000
star
3

U-Mamba

U-Mamba: Enhancing Long-range Dependency for Biomedical Image Segmentation
Python
656
star
4

Graph-Mamba

Graph-Mamba: Towards Long-Range Graph Sequence Modelling with Selective State Spaces
Python
213
star
5

MedSAMSlicer

3D Slicer Plugin for Segment anything in medical images
Python
148
star
6

joint-ner-and-re

This repository contains the corpora and supplementary data, along with instructions for recreating the experiments, for our paper: "End-to-end Named Entity Recognition and Relation Extraction using Pre-trained Language Models".
Jupyter Notebook
91
star
7

ECG-FM

An electrocardiogram analysis foundation model.
Jupyter Notebook
70
star
8

BIONIC

Biological Network Integration using Convolutions
Python
59
star
9

BLEEP

Spatially Resolved Gene Expression Prediction from H&E Histology Images via Bi-modal Contrastive Learning
Python
58
star
10

clinical-camel

Python
49
star
11

DeepVelo

Python
45
star
12

AGILE

AGILE Platform: A Deep Learning-Powered Approach to Accelerate LNP Development for mRNA Delivery
Python
26
star
13

MEDIQA-Chat-2023

A repository for organizing our submission to the MEDIQA-Chat Tasks @ ACL-ClinicalNLP 2023
Python
21
star
14

DPM-MedImgEnhance

Pre-trained Diffusion Models for Plug-and-Play Medical Image Enhancement
Python
20
star
15

scFormer

Python
18
star
16

OCAT

Python
17
star
17

genomic-FM

Python
17
star
18

Transformer-GCN-QA

A multi-hop Q/A architecture based on transformers and GCNs.
Python
15
star
19

MAESTER

Masked Autoencoder Guided Segmentation at Pixel Resolution
Python
15
star
20

CONCERTO

Carcinogenicity prediction with graph neural networks
Jupyter Notebook
10
star
21

LabChat

Jupyter Notebook
10
star
22

CellSeg-Transformers

Python
10
star
23

NanoMASK

mouse pet-ct image segmentation
Python
8
star
24

Transplant_Time_Series

HTML
6
star
25

CongFu

CongFu: Conditional Graph Fusion for Drug Synergy Prediction
Python
6
star
26

IntegrAO

Integrate Any Omics: Towards genome-wide data integration for patient stratification
Jupyter Notebook
6
star
27

simATAC

A single-cell ATAC-seq simulation framework (R package)
R
5
star
28

DES

Single-Shot Object Detection with Enriched Semantics
C++
4
star
29

AMOS-MM-Solution

Solution to the AMOS-MM challenge
Python
4
star
30

SIMLR_PY

Python version of SIMLR
Python
3
star
31

unicell

Universal cellular segmentation models
Python
3
star
32

SIMLR

Single-cell Interpretation via Multi-kernel LeaRning
R
2
star
33

gcn-drug-repurposing

Python
2
star
34

Network_Enhancement

A general method to denoise weighted biological networks
MATLAB
1
star
35

rOCAT

R
1
star
36

shape-attentive-unet

Code for our paper SAUNet: Shape Attentive U-Net for Interpretable Medical Image Segmentation. https://arxiv.org/pdf/2001.07645.pdf
Python
1
star
37

ViST-Echo

PD's thesis work towards a Video Swin Transformer for echocardiographic data.
Python
1
star
38

csc413-2024

Jupyter Notebook
1
star
39

Vicus

Exploiting local structures to improve network-based analysis of biological data
MATLAB
1
star