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
AOT-GAN for High-Resolution Image Inpainting (codebase for image inpainting)

AOT-GAN for High-Resolution Image Inpainting Arxiv Paper | AOT-GAN: Aggregated Contextual Transformations for High-Resolution Image Inpainting Yanhong

Multimedia Research 214 Jan 03, 2023
Self-supervised learning (SSL) is a method of machine learning

Self-supervised learning (SSL) is a method of machine learning. It learns from unlabeled sample data. It can be regarded as an intermediate form between supervised and unsupervised learning.

Ashish Patel 4 May 26, 2022
AdamW optimizer and cosine learning rate annealing with restarts

AdamW optimizer and cosine learning rate annealing with restarts This repository contains an implementation of AdamW optimization algorithm and cosine

Maksym Pyrozhok 133 Dec 20, 2022
Code for the paper "How Attentive are Graph Attention Networks?"

How Attentive are Graph Attention Networks? This repository is the official implementation of How Attentive are Graph Attention Networks?. The PyTorch

175 Dec 29, 2022
Sparse Physics-based and Interpretable Neural Networks

Sparse Physics-based and Interpretable Neural Networks for PDEs This repository contains the code and manuscript for research done on Sparse Physics-b

28 Jan 03, 2023
Continual reinforcement learning baselines: experiment specifications, implementation of existing methods, and common metrics. Easily extensible to new methods.

Continual Reinforcement Learning This repository provides a simple way to run continual reinforcement learning experiments in PyTorch, including evalu

55 Dec 24, 2022
Reproduced Code for Image Forgery Detection papers.

Image Forgery Detection With over 4.5 billion active internet users, the amount of multimedia content being shared every day has surpassed everyone’s

Umar Masud 15 Dec 06, 2022
Discord bot-CTFD-Thread-Parser - Discord bot CTFD-Thread-Parser

Discord bot CTFD-Thread-Parser Description: This tools is used to create automat

15 Mar 22, 2022
I explore rock vs. mine prediction using a SONAR dataset

I explore rock vs. mine prediction using a SONAR dataset. Using a Logistic Regression Model for my prediction algorithm, I intend on predicting what an object is based on supervised learning.

Jeff Shen 1 Jan 11, 2022
NOD: Taking a Closer Look at Detection under Extreme Low-Light Conditions with Night Object Detection Dataset

NOD (Night Object Detection) Dataset NOD: Taking a Closer Look at Detection under Extreme Low-Light Conditions with Night Object Detection Dataset, BM

Igor Morawski 17 Nov 05, 2022
PyTorch implementation of Weak-shot Fine-grained Classification via Similarity Transfer

SimTrans-Weak-Shot-Classification This repository contains the official PyTorch implementation of the following paper: Weak-shot Fine-grained Classifi

BCMI 60 Dec 02, 2022
Learned model to estimate number of distinct values (NDV) of a population using a small sample.

Learned NDV estimator Learned model to estimate number of distinct values (NDV) of a population using a small sample. The model approximates the maxim

2 Nov 21, 2022
Official PyTorch Implementation of Mask-aware IoU and maYOLACT Detector [BMVC2021]

The official implementation of Mask-aware IoU and maYOLACT detector. Our implementation is based on mmdetection. Mask-aware IoU for Anchor Assignment

Kemal Oksuz 46 Sep 29, 2022
Neurons Dataset API - The official dataloader and visualization tools for Neurons Datasets.

Neurons Dataset API - The official dataloader and visualization tools for Neurons Datasets. Introduction We propose our dataloader API for loading and

1 Nov 19, 2021
Pytorch implementation of Compressive Transformers, from Deepmind

Compressive Transformer in Pytorch Pytorch implementation of Compressive Transformers, a variant of Transformer-XL with compressed memory for long-ran

Phil Wang 118 Dec 01, 2022
A library to inspect itermediate layers of PyTorch models.

A library to inspect itermediate layers of PyTorch models. Why? It's often the case that we want to inspect intermediate layers of a model without mod

archinet.ai 380 Dec 28, 2022
Experiments and code to generate the GINC small-scale in-context learning dataset from "An Explanation for In-context Learning as Implicit Bayesian Inference"

GINC small-scale in-context learning dataset GINC (Generative In-Context learning Dataset) is a small-scale synthetic dataset for studying in-context

P-Lambda 29 Dec 19, 2022
Official repository for "Intriguing Properties of Vision Transformers" (2021)

Intriguing Properties of Vision Transformers Muzammal Naseer, Kanchana Ranasinghe, Salman Khan, Munawar Hayat, Fahad Shahbaz Khan, & Ming-Hsuan Yang P

Muzammal Naseer 155 Dec 27, 2022
Pseudo lidar - (CVPR 2019) Pseudo-LiDAR from Visual Depth Estimation: Bridging the Gap in 3D Object Detection for Autonomous Driving

Pseudo-LiDAR from Visual Depth Estimation: Bridging the Gap in 3D Object Detection for Autonomous Driving This paper has been accpeted by Conference o

Yan Wang 881 Dec 27, 2022
Semantic Segmentation in Pytorch

PyTorch Semantic Segmentation Introduction This repository is a PyTorch implementation for semantic segmentation / scene parsing. The code is easy to

Hengshuang Zhao 1.2k Jan 01, 2023