A repository with exploration into using transformers to predict DNA ↔ transcription factor binding

Overview

Transcription Factor binding predictions with Attention and Transformers

A repository with exploration into using transformers to predict DNA transcription factor binding. If you are a researcher interested in this problem, please join the discord server for discussions.

Appreciation

This work is generously sponsored by Jeff Hsu to be done completely open sourced.

You might also like...
Autolfads-tf2 - A TensorFlow 2.0 implementation of Latent Factor Analysis via Dynamical Systems (LFADS) and AutoLFADS

autolfads-tf2 A TensorFlow 2.0 implementation of LFADS and AutoLFADS. Installati

A mini lib that implements several useful functions binding to PyTorch in C++.

Torch-gather A mini library that implements several useful functions binding to PyTorch in C++. What does gather do? Why do we need it? When dealing w

Official implementation of
Official implementation of "Generating 3D Molecules for Target Protein Binding"

Generating 3D Molecules for Target Protein Binding This is the official implementation of the GraphBP method proposed in the following paper. Meng Liu

Patient-Survival - Using Python, I developed a Machine Learning model using classification techniques such as Random Forest and SVM classifiers to predict a patient's survival status that have undergone breast cancer surgery.

Patient-Survival - Using Python, I developed a Machine Learning model using classification techniques such as Random Forest and SVM classifiers to predict a patient's survival status that have undergone breast cancer surgery.

[ICLR 2021] Rank the Episodes: A Simple Approach for Exploration in Procedurally-Generated Environments.
[ICLR 2021] Rank the Episodes: A Simple Approach for Exploration in Procedurally-Generated Environments.

[ICLR 2021] RAPID: A Simple Approach for Exploration in Reinforcement Learning This is the Tensorflow implementation of ICLR 2021 paper Rank the Episo

A mini library for Policy Gradients with Parameter-based Exploration, with reference implementation of the ClipUp optimizer  from NNAISENSE.
A mini library for Policy Gradients with Parameter-based Exploration, with reference implementation of the ClipUp optimizer from NNAISENSE.

PGPElib A mini library for Policy Gradients with Parameter-based Exploration [1] and friends. This library serves as a clean re-implementation of the

Code for the paper Language as a Cognitive Tool to Imagine Goals in Curiosity Driven Exploration
Code for the paper Language as a Cognitive Tool to Imagine Goals in Curiosity Driven Exploration

IMAGINE: Language as a Cognitive Tool to Imagine Goals in Curiosity Driven Exploration This repo contains the code base of the paper Language as a Cog

 Exploration-Exploitation Dilemma Solving Methods
Exploration-Exploitation Dilemma Solving Methods

Exploration-Exploitation Dilemma Solving Methods Medium article for this repo - HERE In ths repo I implemented two techniques for tackling mentioned t

PULSE: Self-Supervised Photo Upsampling via Latent Space Exploration of Generative Models
PULSE: Self-Supervised Photo Upsampling via Latent Space Exploration of Generative Models

PULSE: Self-Supervised Photo Upsampling via Latent Space Exploration of Generative Models Code accompanying CVPR'20 paper of the same title. Paper lin

Releases(v0.0.118)
Owner
Phil Wang
Working with Attention. It's all we need
Phil Wang
(ICCV 2021) Official code of "Dressing in Order: Recurrent Person Image Generation for Pose Transfer, Virtual Try-on and Outfit Editing."

Dressing in Order (DiOr) 👚 [Paper] 👖 [Webpage] 👗 [Running this code] The official implementation of "Dressing in Order: Recurrent Person Image Gene

Aiyu Cui 277 Dec 28, 2022
Few-shot Learning of GPT-3

Few-shot Learning With Language Models This is a codebase to perform few-shot "in-context" learning using language models similar to the GPT-3 paper.

Tony Z. Zhao 224 Dec 28, 2022
Contrastive Language-Image Pretraining

CLIP [Blog] [Paper] [Model Card] [Colab] CLIP (Contrastive Language-Image Pre-Training) is a neural network trained on a variety of (image, text) pair

OpenAI 11.5k Jan 08, 2023
Koç University deep learning framework.

Knet Knet (pronounced "kay-net") is the Koç University deep learning framework implemented in Julia by Deniz Yuret and collaborators. It supports GPU

1.4k Dec 31, 2022
Code for Understanding Pooling in Graph Neural Networks

Select, Reduce, Connect This repository contains the code used for the experiments of: "Understanding Pooling in Graph Neural Networks" Setup Install

Daniele Grattarola 37 Dec 13, 2022
Code repo for "Transformer on a Diet" paper

Transformer on a Diet Reference: C Wang, Z Ye, A Zhang, Z Zhang, A Smola. "Transformer on a Diet". arXiv preprint arXiv (2020). Installation pip insta

cgraywang 31 Sep 26, 2021
Pytorch Implementation of paper "Noisy Natural Gradient as Variational Inference"

Noisy Natural Gradient as Variational Inference PyTorch implementation of Noisy Natural Gradient as Variational Inference. Requirements Python 3 Pytor

Tony JiHyun Kim 119 Dec 02, 2022
Performant, differentiable reinforcement learning

deluca Performant, differentiable reinforcement learning Notes This is pre-alpha software and is undergoing a number of core changes. Updates to follo

Google 114 Dec 27, 2022
PassAPI is a password generator in hash format and fully developed in Python, with the aim of teaching how to handle and build

simple, elegant and safe Introduction PassAPI is a password generator in hash format and fully developed in Python, with the aim of teaching how to ha

Johnsz 2 Mar 02, 2022
A PyTorch implementation of "Multi-Scale Contrastive Siamese Networks for Self-Supervised Graph Representation Learning", IJCAI-21

MERIT A PyTorch implementation of our IJCAI-21 paper Multi-Scale Contrastive Siamese Networks for Self-Supervised Graph Representation Learning. Depen

Graph Analysis & Deep Learning Laboratory, GRAND 32 Jan 02, 2023
A simple algorithm for extracting tree height in sparse scene from point cloud data.

TREE HEIGHT EXTRACTION IN SPARSE SCENES BASED ON UAV REMOTE SENSING This is the offical python implementation of the paper "Tree Height Extraction in

6 Oct 28, 2022
Pytorch implementation of "Training a 85.4% Top-1 Accuracy Vision Transformer with 56M Parameters on ImageNet"

Token Labeling: Training an 85.4% Top-1 Accuracy Vision Transformer with 56M Parameters on ImageNet (arxiv) This is a Pytorch implementation of our te

蒋子航 383 Dec 27, 2022
Graph-total-spanning-trees - A Python script to get total number of Spanning Trees in a Graph

Total number of Spanning Trees in a Graph This is a python script just written f

Mehdi I. 0 Jul 18, 2022
nfelo: a power ranking, prediction, and betting model for the NFL

nfelo nfelo is a power ranking, prediction, and betting model for the NFL. Nfelo take's 538's Elo framework and further adapts it for the NFL, hence t

6 Nov 22, 2022
SberSwap Video Swap base on deep learning

SberSwap Video Swap base on deep learning

Sber AI 431 Jan 03, 2023
LBK 26 Dec 28, 2022
The code for "Deep Level Set for Box-supervised Instance Segmentation in Aerial Images".

Deep Levelset for Box-supervised Instance Segmentation in Aerial Images Wentong Li, Yijie Chen, Wenyu Liu, Jianke Zhu* This code is based on MMdetecti

sunshine.lwt 112 Jan 05, 2023
Face recognition project by matching the features extracted using SIFT.

MV_FaceDetectionWithSIFT Face recognition project by matching the features extracted using SIFT. By : Aria Radmehr Professor : Ali Amiri Dependencies

Aria Radmehr 4 May 31, 2022
Code and real data for the paper "Counterfactual Temporal Point Processes", available at arXiv.

counterfactual-tpp This is a repository containing code and real data for the paper Counterfactual Temporal Point Processes. Pre-requisites This code

Networks Learning 11 Dec 09, 2022
Py-FEAT: Python Facial Expression Analysis Toolbox

Py-FEAT is a suite for facial expressions (FEX) research written in Python. This package includes tools to detect faces, extract emotional facial expressions (e.g., happiness, sadness, anger), facial

Computational Social Affective Neuroscience Laboratory 147 Jan 06, 2023