XIE LAB @ UCI

NoduleNet

[MICCAI' 19] NoduleNet: Decoupled False Positive Reduction for Pulmonary Nodule Detection and Segmentation

DanQ

A hybrid convolutional and recurrent neural network for predicting the function of DNA sequences

DeepLung

WACV18 paper "DeepLung: Deep 3D Dual Path Nets for Automated Pulmonary Nodule Detection and Classification"

D-GEX

Deep learning for gene expression inference

UaNet

UFold

RP-Net

Code for Recurrent Mask Refinement for Few-Shot Medical Image Segmentation (ICCV 2021).

FactorNet

A deep learning package for predicting TF binding

PyLOH

Deconvolving tumor purity and ploidy by integrating copy number alterations and loss of heterozygosity

EXTREME

An online EM implementation of the MEME model for fast motif discovery in large ChIP-Seq and DNase-Seq Footprinting data

HLA-bind

Amino acid embedding and Convolutional Neural Network for HLA Class I-peptide binding prediction

DeepCons

Understanding sequence conservation with deep learning

DeepEM-for-Weakly-Supervised-Detection-1

MICCAI18 DeepEM: Deep 3D ConvNets with EM for Weakly Supervised Pulmonary Nodule Detection

DeepEM-for-Weakly-Supervised-Detection

MICCAI18 DeepEM: Deep 3D ConvNets with EM for Weakly Supervised Pulmonary Nodule Detection

BioML

ChestXRay

MixClone

A mixture model for inferring tumor subclonal populations

SAILER

TEMT

Transcripts abundances estimation from heterogeneous tissue sample of RNA-Seq data (TEMT)

genomix

Parallel genome assembly using Hyracks

SAILERX

scFAN

EpiOut

A statistical method to detect, analyze and visualize aberrations in chromatin accessibility (ATAC-seq, DNase-Seq) and quantify its effect on gene expression.

RBPnet

ChromDEEP

Chromatin states analysis with deep learning

ConsDEEP

Sequence conservatoin analysis with deep learning

CoreNLP

Stanford CoreNLP: A Java suite of core NLP tools.

DEEMOL

Deep learning for molecular modelling

polyAcode

Video-Pre-Training

Video PreTraining (VPT): Learning to Act by Watching Unlabeled Online Videos