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] Encoder-decoder with Multi-level Attention for 3D Human Shape and Pose Estimation

MAED: Encoder-decoder with Multi-level Attention for 3D Human Shape and Pose Estimation Getting Started Our codes are implemented and tested with pyth

ZiNiU WaN 176 Dec 15, 2022
A GUI for Face Recognition, based upon Docker, Tkinter, GPU and a camera device.

Face Recognition GUI This repository is a GUI version of Face Recognition by Adam Geitgey, where e.g. Docker and Tkinter are utilized. All the materia

Kasper Henriksen 6 Dec 05, 2022
Official implementation of Rethinking Graph Neural Architecture Search from Message-passing (CVPR2021)

Rethinking Graph Neural Architecture Search from Message-passing Intro The GNAS can automatically learn better architecture with the optimal depth of

Shaofei Cai 48 Sep 30, 2022
"Neural Turing Machine" in Tensorflow

Neural Turing Machine in Tensorflow Tensorflow implementation of Neural Turing Machine. This implementation uses an LSTM controller. NTM models with m

Taehoon Kim 1k Dec 06, 2022
World Models with TensorFlow 2

World Models This repo reproduces the original implementation of World Models. This implementation uses TensorFlow 2.2. Docker The easiest way to hand

Zac Wellmer 234 Nov 30, 2022
NOMAD - A blackbox optimization software

################################################################################### #

Blackbox Optimization 78 Dec 29, 2022
The code for SAG-DTA: Prediction of Drug–Target Affinity Using Self-Attention Graph Network.

SAG-DTA The code is the implementation for the paper 'SAG-DTA: Prediction of Drug–Target Affinity Using Self-Attention Graph Network'. Requirements py

Shugang Zhang 7 Aug 02, 2022
This repository is an unoffical PyTorch implementation of Medical segmentation in 3D and 2D.

Pytorch Medical Segmentation Read Chinese Introduction:Here! Recent Updates 2021.1.8 The train and test codes are released. 2021.2.6 A bug in dice was

EasyCV-Ellis 618 Dec 27, 2022
PyTorch Implementation of Spatially Consistent Representation Learning(SCRL)

Spatially Consistent Representation Learning (CVPR'21) Official PyTorch implementation of Spatially Consistent Representation Learning (SCRL). This re

Kakao Brain 102 Nov 03, 2022
A Benchmark For Measuring Systematic Generalization of Multi-Hierarchical Reasoning

Orchard Dataset This repository contains the code used for generating the Orchard Dataset, as seen in the Multi-Hierarchical Reasoning in Sequences: S

Bill Pung 1 Jun 05, 2022
Jigsaw Rate Severity of Toxic Comments

Jigsaw Rate Severity of Toxic Comments

Guanshuo Xu 66 Nov 30, 2022
Learning Multiresolution Matrix Factorization and its Wavelet Networks on Graphs

Project Learning Multiresolution Matrix Factorization and its Wavelet Networks on Graphs, https://arxiv.org/pdf/2111.01940.pdf. Authors Truong Son Hy

5 Jun 28, 2022
This implements one of result networks from Large-scale evolution of image classifiers

Exotic structured image classifier This implements one of result networks from Large-scale evolution of image classifiers by Esteban Real, et. al. Req

54 Nov 25, 2022
Code for "CloudAAE: Learning 6D Object Pose Regression with On-line Data Synthesis on Point Clouds" @ICRA2021

CloudAAE This is an tensorflow implementation of "CloudAAE: Learning 6D Object Pose Regression with On-line Data Synthesis on Point Clouds" Files log:

Gee 35 Nov 14, 2022
HandFoldingNet ✌️ : A 3D Hand Pose Estimation Network Using Multiscale-Feature Guided Folding of a 2D Hand Skeleton

HandFoldingNet ✌️ : A 3D Hand Pose Estimation Network Using Multiscale-Feature Guided Folding of a 2D Hand Skeleton Wencan Cheng, Jae Hyun Park, Jong

cwc1260 23 Oct 21, 2022
Localized representation learning from Vision and Text (LoVT)

Localized Vision-Text Pre-Training Contrastive learning has proven effective for pre- training image models on unlabeled data and achieved great resul

Philip Müller 10 Dec 07, 2022
Implementation for the paper SMPLicit: Topology-aware Generative Model for Clothed People (CVPR 2021)

SMPLicit: Topology-aware Generative Model for Clothed People [Project] [arXiv] License Software Copyright License for non-commercial scientific resear

Enric Corona 225 Dec 13, 2022
FairEdit: Preserving Fairness in Graph Neural Networks through Greedy Graph Editing

FairEdit Relevent Publication FairEdit: Preserving Fairness in Graph Neural Networks through Greedy Graph Editing

5 Feb 04, 2022
Ranger deep learning optimizer rewrite to use newest components

Ranger21 - integrating the latest deep learning components into a single optimizer Ranger deep learning optimizer rewrite to use newest components Ran

Less Wright 266 Dec 28, 2022
Full body anonymization - Realistic Full-Body Anonymization with Surface-Guided GANs

Realistic Full-Body Anonymization with Surface-Guided GANs This is the official

Håkon Hukkelås 30 Nov 18, 2022