Equivariant layers for RC-complement symmetry in DNA sequence data

Related tags

Deep LearningEqui-RC
Overview

Equi-RC

Equivariant layers for RC-complement symmetry in DNA sequence data

This is a repository that implements the layers as described in "Reverse-Complement Equivariant Networks for DNA Sequences" in Keras and Pytorch. The simplest way to use it is to include the appropriate standalone python script in your code.

Setup and notes

Just install Keras or Pytorch and you can start importing the layers.

The reg_in, reg_out arguments should be understood as the number of cycles. This correspond to half the input dimension (so for the input, we have 4 nucleotides, so reg=2)

The a_n are of the dimensions of type +1, the b_n of type -1

Examples

Keras

This class used for the Binary Prediction task is implemented as an example. One can refer to this implementation and for testing, simply run :

python keras_example.py

Pytorch

The equivalent class is also written in Pytorch, and can be ran with :

python pytorch_example.py
Subnet Replacement Attack: Towards Practical Deployment-Stage Backdoor Attack on Deep Neural Networks

Subnet Replacement Attack: Towards Practical Deployment-Stage Backdoor Attack on Deep Neural Networks Official implementation of paper Towards Practic

Xiangyu Qi 8 Dec 30, 2022
A crash course in six episodes for software developers who want to become machine learning practitioners.

Featured code sample tensorflow-planespotting Code from the Google Cloud NEXT 2018 session "Tensorflow, deep learning and modern convnets, without a P

Google Cloud Platform 2.6k Jan 08, 2023
Audio Domain Adaptation for Acoustic Scene Classification using Disentanglement Learning

Audio Domain Adaptation for Acoustic Scene Classification using Disentanglement Learning Reference Abeßer, J. & Müller, M. Towards Audio Domain Adapt

Jakob Abeßer 2 Jul 06, 2022
An extremely simple, intuitive, hardware-friendly, and well-performing network structure for LiDAR semantic segmentation on 2D range image. IROS21

FIDNet_SemanticKITTI Motivation Implementing complicated network modules with only one or two points improvement on hardware is tedious. So here we pr

YimingZhao 54 Dec 12, 2022
Generalized Decision Transformer for Offline Hindsight Information Matching

Generalized Decision Transformer for Offline Hindsight Information Matching [arxiv] If you use this codebase for your research, please cite the paper:

Hiroki Furuta 35 Dec 12, 2022
Learning 3D Part Assembly from a Single Image

Learning 3D Part Assembly from a Single Image This repository contains a PyTorch implementation of the paper: Learning 3D Part Assembly from A Single

18 Dec 21, 2022
Implementation of Sequence Generative Adversarial Nets with Policy Gradient

SeqGAN Requirements: Tensorflow r1.0.1 Python 2.7 CUDA 7.5+ (For GPU) Introduction Apply Generative Adversarial Nets to generating sequences of discre

Lantao Yu 2k Dec 29, 2022
Pytorch implemenation of Stochastic Multi-Label Image-to-image Translation (SMIT)

SMIT: Stochastic Multi-Label Image-to-image Translation This repository provides a PyTorch implementation of SMIT. SMIT can stochastically translate a

Biomedical Computer Vision Group @ Uniandes 37 Mar 01, 2022
Toolchain to build Yoshi's Island from source code

Project-Y Toolchain to build Yoshi's Island (J) V1.0 from source code, by MrL314 Last updated: September 17, 2021 Setup To begin, download this toolch

MrL314 19 Apr 18, 2022
Jittor is a high-performance deep learning framework based on JIT compiling and meta-operators.

Jittor: a Just-in-time(JIT) deep learning framework Quickstart | Install | Tutorial | Chinese Jittor is a high-performance deep learning framework bas

2.7k Jan 03, 2023
Covid19-Forecasting - An interactive website that tracks, models and predicts COVID-19 Cases

Covid-Tracker This is an interactive website that tracks, models and predicts CO

Adam Lahmadi 1 Feb 01, 2022
PyTorch implementation of Glow

glow-pytorch PyTorch implementation of Glow, Generative Flow with Invertible 1x1 Convolutions (https://arxiv.org/abs/1807.03039) Usage: python train.p

Kim Seonghyeon 433 Dec 27, 2022
Roadmap to becoming a machine learning engineer in 2020

Roadmap to becoming a machine learning engineer in 2020, inspired by web-developer-roadmap.

Chris Hoyean Song 1.7k Dec 29, 2022
Contrastive learning of Class-agnostic Activation Map for Weakly Supervised Object Localization and Semantic Segmentation (CVPR 2022)

CCAM (Unsupervised) Code repository for our paper "CCAM: Contrastive learning of Class-agnostic Activation Map for Weakly Supervised Object Localizati

Computer Vision Insitute, SZU 113 Dec 27, 2022
QA-GNN: Question Answering using Language Models and Knowledge Graphs

QA-GNN: Question Answering using Language Models and Knowledge Graphs This repo provides the source code & data of our paper: QA-GNN: Reasoning with L

Michihiro Yasunaga 434 Jan 04, 2023
NVIDIA Merlin is an open source library providing end-to-end GPU-accelerated recommender systems, from feature engineering and preprocessing to training deep learning models and running inference in production.

NVIDIA Merlin NVIDIA Merlin is an open source library designed to accelerate recommender systems on NVIDIA’s GPUs. It enables data scientists, machine

419 Jan 03, 2023
:hot_pepper: R²SQL: "Dynamic Hybrid Relation Network for Cross-Domain Context-Dependent Semantic Parsing." (AAAI 2021)

R²SQL The PyTorch implementation of paper Dynamic Hybrid Relation Network for Cross-Domain Context-Dependent Semantic Parsing. (AAAI 2021) Requirement

huybery 60 Dec 31, 2022
End-to-End Dense Video Captioning with Parallel Decoding (ICCV 2021)

PDVC Official implementation for End-to-End Dense Video Captioning with Parallel Decoding (ICCV 2021) [paper] [valse论文速递(Chinese)] This repo supports:

Teng Wang 118 Dec 16, 2022
Locally Differentially Private Distributed Deep Learning via Knowledge Distillation (LDP-DL)

Locally Differentially Private Distributed Deep Learning via Knowledge Distillation (LDP-DL) A preprint version of our paper: Link here This is a samp

Di Zhuang 3 Jan 08, 2023
Beyond Image to Depth: Improving Depth Prediction using Echoes (CVPR 2021)

Beyond Image to Depth: Improving Depth Prediction using Echoes (CVPR 2021) Kranti Kumar Parida, Siddharth Srivastava, Gaurav Sharma. We address the pr

Kranti Kumar Parida 33 Jun 27, 2022