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
Open-Ended Commonsense Reasoning (NAACL 2021)

Open-Ended Commonsense Reasoning Quick links: [Paper] | [Video] | [Slides] | [Documentation] This is the repository of the paper, Differentiable Open-

(Bill) Yuchen Lin 31 Oct 19, 2022
Official Implementation for "ReStyle: A Residual-Based StyleGAN Encoder via Iterative Refinement" https://arxiv.org/abs/2104.02699

ReStyle: A Residual-Based StyleGAN Encoder via Iterative Refinement Recently, the power of unconditional image synthesis has significantly advanced th

967 Jan 04, 2023
😇A pyTorch implementation of the DeepMoji model: state-of-the-art deep learning model for analyzing sentiment, emotion, sarcasm etc

------ Update September 2018 ------ It's been a year since TorchMoji and DeepMoji were released. We're trying to understand how it's being used such t

Hugging Face 865 Dec 24, 2022
TorchCV: A PyTorch-Based Framework for Deep Learning in Computer Vision

TorchCV: A PyTorch-Based Framework for Deep Learning in Computer Vision @misc{you2019torchcv, author = {Ansheng You and Xiangtai Li and Zhen Zhu a

Donny You 2.2k Jan 06, 2023
Geometric Algebra package for JAX

JAXGA - JAX Geometric Algebra GitHub | Docs JAXGA is a Geometric Algebra package on top of JAX. It can handle high dimensional algebras by storing onl

Robin Kahlow 36 Dec 22, 2022
ICLR 2021: Pre-Training for Context Representation in Conversational Semantic Parsing

SCoRe: Pre-Training for Context Representation in Conversational Semantic Parsing This repository contains code for the ICLR 2021 paper "SCoRE: Pre-Tr

Microsoft 28 Oct 02, 2022
Pytorch modules for paralel models with same architecture. Ideal for multi agent-based systems

WideLinears Pytorch parallel Neural Networks A package of pytorch modules for fast paralellization of separate deep neural networks. Ideal for agent-b

1 Dec 17, 2021
Supervised forecasting of sequential data in Python.

Supervised forecasting of sequential data in Python. Intro Supervised forecasting is the machine learning task of making predictions for sequential da

The Alan Turing Institute 54 Nov 15, 2022
MagFace: A Universal Representation for Face Recognition and Quality Assessment

MagFace MagFace: A Universal Representation for Face Recognition and Quality Assessment in IEEE Conference on Computer Vision and Pattern Recognition

Qiang Meng 523 Jan 05, 2023
Cockpit is a visual and statistical debugger specifically designed for deep learning.

Cockpit: A Practical Debugging Tool for Training Deep Neural Networks

Felix Dangel 421 Dec 29, 2022
FairyTailor: Multimodal Generative Framework for Storytelling

FairyTailor: Multimodal Generative Framework for Storytelling

Eden Bens 172 Dec 30, 2022
The coda and data for "Measuring Fine-Grained Domain Relevance of Terms: A Hierarchical Core-Fringe Approach" (ACL '21)

We propose a hierarchical core-fringe learning framework to measure fine-grained domain relevance of terms – the degree that a term is relevant to a broad (e.g., computer science) or narrow (e.g., de

Jie Huang 14 Oct 21, 2022
This repo includes the CUB-GHA (Gaze-based Human Attention) dataset and code of the paper "Human Attention in Fine-grained Classification".

HA-in-Fine-Grained-Classification This repo includes the CUB-GHA (Gaze-based Human Attention) dataset and code of the paper "Human Attention in Fine-g

16 Oct 29, 2022
LSTC: Boosting Atomic Action Detection with Long-Short-Term Context

LSTC: Boosting Atomic Action Detection with Long-Short-Term Context This Repository contains the code on AVA of our ACM MM 2021 paper: LSTC: Boosting

Tencent YouTu Research 9 Oct 11, 2022
A Python package for causal inference using Synthetic Controls

Synthetic Control Methods A Python package for causal inference using synthetic controls This Python package implements a class of approaches to estim

Oscar Engelbrektson 107 Dec 28, 2022
Official PyTorch Implementation of HELP: Hardware-adaptive Efficient Latency Prediction for NAS via Meta-Learning (NeurIPS 2021 Spotlight)

[NeurIPS 2021 Spotlight] HELP: Hardware-adaptive Efficient Latency Prediction for NAS via Meta-Learning [Paper] This is Official PyTorch implementatio

42 Nov 01, 2022
The open-source and free to use Python package miseval was developed to establish a standardized medical image segmentation evaluation procedure

miseval: a metric library for Medical Image Segmentation EVALuation The open-source and free to use Python package miseval was developed to establish

59 Dec 10, 2022
ROMP: Monocular, One-stage, Regression of Multiple 3D People, ICCV21

Monocular, One-stage, Regression of Multiple 3D People ROMP, accepted by ICCV 2021, is a concise one-stage network for multi-person 3D mesh recovery f

Yu Sun 937 Jan 04, 2023
The Pytorch implementation for "Video-Text Pre-training with Learned Regions"

Region_Learner The Pytorch implementation for "Video-Text Pre-training with Learned Regions" (arxiv) We are still cleaning up the code further and pre

Rui Yan 0 Mar 20, 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* Any questions or discussions ar

sunshine.lwt 112 Jan 05, 2023