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

Related tags

Deep Learningtranscription-factorsdeep-learningtransformersgene-expressionartificial-intelligencetranscription-factor-bindingattention-mechanism
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

Systems Neural Engineering Lab 11 Oct 29, 2022
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

maxwellzh 8 Sep 7, 2022
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

DIVE Lab, Texas A&M University 74 Dec 7, 2022
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.

Nafis Ahmed 1 Dec 28, 2021
[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

Daochen Zha 48 Nov 21, 2022
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

NNAISENSE 56 Jan 1, 2023
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

Flowers Team 26 Dec 22, 2022
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

Aman Mishra 6 Jan 25, 2022
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

Alex Damian 7k Dec 30, 2022
Releases(v0.0.118)
Owner
Phil Wang
Working with Attention. It's all we need
Phil Wang
GitHub Repository
Camera calibration & 3D pose estimation tools for AcinoSet

AcinoSet: A 3D Pose Estimation Dataset and Baseline Models for Cheetahs in the Wild Daniel Joska, Liam Clark, Naoya Muramatsu, Ricardo Jericevich, Fre

African Robotics Unit 42 Nov 16, 2022
Crosslingual Segmental Language Model

Crosslingual Segmental Language Model This repository contains the code from Multilingual unsupervised sequence segmentation transfers to extremely lo

C.M. Downey 1 Jun 13, 2022
Deep deconfounded recommender (Deep-Deconf) for paper "Deep causal reasoning for recommendations"

Deep Causal Reasoning for Recommender Systems The codes are associated with the following paper: Deep Causal Reasoning for Recommendations, Yaochen Zh

Yaochen Zhu 22 Oct 15, 2022
Code of Classification Saliency-Based Rule for Visible and Infrared Image Fusion

CSF Code of Classification Saliency-Based Rule for Visible and Infrared Image Fusion Tips: For testing: CUDA_VISIBLE_DEVICES=0 python main.py For trai

Han Xu 14 Oct 31, 2022
This repository builds a basic vision transformer from scratch so that one beginner can understand the theory of vision transformer.

vision-transformer-from-scratch This repository includes several kinds of vision transformers from scratch so that one beginner can understand the the

1 Dec 24, 2021
Bayesian optimization in PyTorch

BoTorch is a library for Bayesian Optimization built on PyTorch. BoTorch is currently in beta and under active development! Why BoTorch ? BoTorch Prov

2.5k Dec 31, 2022
The official repository for BaMBNet

BaMBNet-Pytorch Paper

Junjun Jiang 18 Dec 04, 2022
ZSL-KG is a general-purpose zero-shot learning framework with a novel transformer graph convolutional network (TrGCN) to learn class representation from common sense knowledge graphs.

ZSL-KG is a general-purpose zero-shot learning framework with a novel transformer graph convolutional network (TrGCN) to learn class representa

Bats Research 94 Nov 21, 2022
StackNet is a computational, scalable and analytical Meta modelling framework

StackNet This repository contains StackNet Meta modelling methodology (and software) which is part of my work as a PhD Student in the computer science

Marios Michailidis 1.3k Dec 15, 2022
Efficient Training of Audio Transformers with Patchout

PaSST: Efficient Training of Audio Transformers with Patchout This is the implementation for Efficient Training of Audio Transformers with Patchout Pa

165 Dec 26, 2022
Stacs-ci - A set of modules to enable integration of STACS with commonly used CI / CD systems

Static Token And Credential Scanner CI Integrations What is it? STACS is a YARA

STACS 18 Aug 04, 2022
MonoRCNN is a monocular 3D object detection method for automonous driving

MonoRCNN MonoRCNN is a monocular 3D object detection method for automonous driving, published at ICCV 2021. This project is an implementation of MonoR

87 Dec 27, 2022
Scale-aware Automatic Augmentation for Object Detection (CVPR 2021)

SA-AutoAug Scale-aware Automatic Augmentation for Object Detection Yukang Chen, Yanwei Li, Tao Kong, Lu Qi, Ruihang Chu, Lei Li, Jiaya Jia [Paper] [Bi

DV Lab 182 Dec 29, 2022
FID calculation with proper image resizing and quantization steps

clean-fid: Fixing Inconsistencies in FID Project | Paper The FID calculation involves many steps that can produce inconsistencies in the final metric.

Gaurav Parmar 606 Jan 06, 2023
Converting CPT to bert form for use

cpt-encoder 将CPT转成bert形式使用 说明 刚刚刷到又出了一种模型：CPT，看论文显示，在很多中文任务上性能比mac bert还好，就迫不及待想把它用起来。 根据对源码的研究，发现该模型在做nlu建模时主要用的encoder部分，也就是bert，因此我将这部分权重转为bert权重类型

黄辉 1 Oct 14, 2021
[ICCV21] Code for RetrievalFuse: Neural 3D Scene Reconstruction with a Database

RetrievalFuse Paper | Project Page | Video RetrievalFuse: Neural 3D Scene Reconstruction with a Database Yawar Siddiqui, Justus Thies, Fangchang Ma, Q

Yawar Nihal Siddiqui 75 Dec 22, 2022
[CVPR21] LightTrack: Finding Lightweight Neural Network for Object Tracking via One-Shot Architecture Search

LightTrack: Finding Lightweight Neural Networks for Object Tracking via One-Shot Architecture Search The official implementation of the paper LightTra

Multimedia Research 290 Dec 24, 2022
Generate indoor scenes with Transformers

SceneFormer: Indoor Scene Generation with Transformers Initial code release for the Sceneformer paper, contains models, train and test scripts for the

Chandan Yeshwanth 110 Dec 06, 2022
MinkLoc++: Lidar and Monocular Image Fusion for Place Recognition

MinkLoc++: Lidar and Monocular Image Fusion for Place Recognition Paper: MinkLoc++: Lidar and Monocular Image Fusion for Place Recognition accepted fo

64 Dec 18, 2022
DeepFaceLive - Live Deep Fake in python, Real-time face swap for PC streaming or video calls

DeepFaceLive - Live Deep Fake in python, Real-time face swap for PC streaming or video calls

8.3k Dec 31, 2022