Implementation of Neural Distance Embeddings for Biological Sequences (NeuroSEED) in PyTorch

Overview

Neural Distance Embeddings for Biological Sequences

Official implementation of Neural Distance Embeddings for Biological Sequences (NeuroSEED) in PyTorch. NeuroSEED is a novel framework to embed biological sequences in geometric vector spaces. Preprint will we published soon.

diagram

Overview

The repository is organised in four main folders one for each of the tasks analysed. Each of these contain scripts and models used for the task as well as instructions on how to run them and the tuned hyperparameters found.

  • edit_distance for the edit distance approximation task
  • closest_string for the closest string retrieval task
  • hierarchical_clustering for the hierarchical clustering task, further divided in relaxed and unsupervised for the two approaches explored
  • multiple_alignment for the multiple sequence alignment task, further divided in guide_tree and steiner_string
  • util contains a series of utility routines shared between all the tasks
  • tests contains a wide range of tests for the various components of the repository

Installation

Create a virtual (or conda) environment and install the dependencies:

python3 -m venv neuroseed
source neuroseed/bin/activate
pip install -r requirements.txt

Then install the mst and unionfind packages used for the hierarchical clustering:

cd hierarchical_clustering/relaxed/mst; python setup.py build_ext --inplace; cd ../../..
cd hierarchical_clustering/relaxed/unionfind; python setup.py build_ext --inplace; cd ../../..

License

MIT

Owner
Gabriele Corso
PhD student @ MIT • Research on Graph and Geometric Representation Learning • Previously intern @ Twitter Research, D.E. Shaw and IBM
Gabriele Corso
A tensorflow implementation of GCN-LPA

GCN-LPA This repository is the implementation of GCN-LPA (arXiv): Unifying Graph Convolutional Neural Networks and Label Propagation Hongwei Wang, Jur

Hongwei Wang 83 Nov 28, 2022
Learning to Prompt for Vision-Language Models.

CoOp Paper: Learning to Prompt for Vision-Language Models Authors: Kaiyang Zhou, Jingkang Yang, Chen Change Loy, Ziwei Liu CoOp (Context Optimization)

Kaiyang 679 Jan 04, 2023
A denoising diffusion probabilistic model synthesises galaxies that are qualitatively and physically indistinguishable from the real thing.

Realistic galaxy simulation via score-based generative models Official code for 'Realistic galaxy simulation via score-based generative models'. We us

Michael Smith 32 Dec 20, 2022
Yolo algorithm for detection + centroid tracker to track vehicles

Vehicle Tracking using Centroid tracker Algorithm used : Yolo algorithm for detection + centroid tracker to track vehicles Backend : opencv and python

6 Dec 21, 2022
Music Classification: Beyond Supervised Learning, Towards Real-world Applications

Music Classification: Beyond Supervised Learning, Towards Real-world Applications

104 Dec 15, 2022
Tutorials and implementations for "Self-normalizing networks"

Self-Normalizing Networks Tutorials and implementations for "Self-normalizing networks"(SNNs) as suggested by Klambauer et al. (arXiv pre-print). Vers

Institute of Bioinformatics, Johannes Kepler University Linz 1.6k Jan 07, 2023
Embracing Single Stride 3D Object Detector with Sparse Transformer

SST: Single-stride Sparse Transformer This is the official implementation of paper: Embracing Single Stride 3D Object Detector with Sparse Transformer

TuSimple 385 Dec 28, 2022
VR Viewport Pose Model for Quantifying and Exploiting Frame Correlations

This repository contains the introduction to the collected VRViewportPose dataset and the code for the IEEE INFOCOM 2022 paper: "VR Viewport Pose Model for Quantifying and Exploiting Frame Correlatio

0 Aug 10, 2022
Segmentation models with pretrained backbones. Keras and TensorFlow Keras.

Python library with Neural Networks for Image Segmentation based on Keras and TensorFlow. The main features of this library are: High level API (just

Pavel Yakubovskiy 4.2k Jan 09, 2023
Tool for working with Y-chromosome data from YFull and FTDNA

ycomp ycomp is a tool for working with Y-chromosome data from YFull and FTDNA. Run ycomp -h for information on how to use the program. Installation Th

Alexander Regueiro 2 Jun 18, 2022
TensorRT examples (Jetson, Python/C++)(object detection)

TensorRT examples (Jetson, Python/C++)(object detection)

Nobuo Tsukamoto 53 Dec 22, 2022
🔮 A refreshing functional take on deep learning, compatible with your favorite libraries

Thinc: A refreshing functional take on deep learning, compatible with your favorite libraries From the makers of spaCy, Prodigy and FastAPI Thinc is a

Explosion 2.6k Dec 30, 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
Object Detection with YOLOv3

Object Detection with YOLOv3 Bu projede YOLOv3-608 modeli kullanılmıştır. Requirements Python 3.8 OpenCV Numpy Documentation Yolo ile ilgili detaylı b

Ayşe Konuş 0 Mar 27, 2022
The code used for the free [email protected] Webinar series on Reinforcement Learning in Finance

Reinforcement Learning in Finance [email protected] Webinar This repository provides the code f

Yves Hilpisch 62 Dec 22, 2022
ImVoxelNet: Image to Voxels Projection for Monocular and Multi-View General-Purpose 3D Object Detection

ImVoxelNet: Image to Voxels Projection for Monocular and Multi-View General-Purpose 3D Object Detection This repository contains implementation of the

Visual Understanding Lab @ Samsung AI Center Moscow 190 Dec 30, 2022
Implementation of Artificial Neural Network Algorithm

Artificial Neural Network This repository contain implementation of Artificial Neural Network Algorithm in several programming languanges and framewor

Resha Dwika Hefni Al-Fahsi 1 Sep 14, 2022
MPI-IS Mesh Processing Library

Perceiving Systems Mesh Package This package contains core functions for manipulating meshes and visualizing them. It requires Python 3.5+ and is supp

Max Planck Institute for Intelligent Systems 494 Jan 06, 2023
Code for the TIP 2021 Paper "Salient Object Detection with Purificatory Mechanism and Structural Similarity Loss"

PurNet Project for the TIP 2021 Paper "Salient Object Detection with Purificatory Mechanism and Structural Similarity Loss" Abstract Image-based salie

Jinming Su 4 Aug 25, 2022
Sequential model-based optimization with a `scipy.optimize` interface

Scikit-Optimize Scikit-Optimize, or skopt, is a simple and efficient library to minimize (very) expensive and noisy black-box functions. It implements

Scikit-Optimize 2.5k Jan 04, 2023