Code for the Nature Scientific Reports paper "Pathologist-level classification of histologic patterns on resected lung adenocarcinoma slides with deep neural networks." A sliding window framework for classification of high resolution whole-slide images, often microscopy or histopathology images.

Personalized Genomics and Proteomics. Main diet: Ensembl, side dishes: SNPs

Opensource Python project for cancer radiation treatment planning [AAPM'23]

The official implementation of GPFM

A Slicer extension to provide a GUI around pyradiomics

A quickstart tool for AmpliconArchitect. Enables all steps (alignment, CNV calling, seed interval detection) prior to running AmpliconArchitect, and invokes AmpliconClassifier

Python package to annotate and visualize gene fusions.

MADELEINE: multi-stain slide representation learning (ECCV'24)

Predicting multiple cancer phenotypes based on somatic genomic alterations via the genomic impact transformer

Multi-task deep learning framework for multi-omics data analysis

Classifies genes as an oncogene, tumor suppressor gene, or as a non-driver gene by using Random Forests

[IEEE TMI] Tumor synthesis leveraging medical reports.

Flask App for Cancer Donation Portal using basic Python, SQLite3, HTML, CSS and Javascript

Method for Identifying Novel Transcripts and Isoforms using Equivalence classes, in cancer and rare disease.

A Python-Tensorflow neural network for classifying cancer data

Synthetic lethality (SL) is a promising gold mine for the discovery of anti-cancer drug targets. KG4SL is the first graph neural network (GNN)-based model that uses knowledge graph for SL prediction.

Pulmonary nodules computer-aided diagnosis demo system.

Text mining cancer biomarkers for the CIVIC database

PFA-ScanNet: Pyramidal Feature Aggregation With Synergistic Learning for Breast Cancer Metastasis Analysis (Architecture Only Pytorch Implementation).