Improved Fitness Optimization Landscapes for Sequence Design

Overview

ReLSO

Improved Fitness Optimization Landscapes for Sequence Design

Description


In recent years, deep learning approaches for determining protein sequence-fitness relationships have gained traction. Advances in high-throughput mutagenesis, directed evolution, and next-generation sequencing have allowed for the accumulation of large amounts of labelled fitness data and consequently, attracted the application of various deep learning methods. Although these methods learn an implicit fitness landscape, there is little work on using the latent encoding directly for protein sequence optimization. Here we show that this latent space representation of a fitness landscape can be made very amenable to latent space optimization through a joint-training process. We also show that this encoding strategy which also provides improvements to generalization over more traditional training strategies. We apply our approach to several biological contexts and show that latent space optimization in a smooth learned folding landscape allows for more accurate and efficient optimization of protein sequences.

Citation

This repo accompanies the following publication:

Egbert Castro, Abhinav Godavarthi, Julien Rubinfien, Smita Krishnaswamy. Guided Generative Protein Design using Regularized Transformers. Nature Machine Intelligence, in review (2021).

How to run


First, install dependencies

# clone project   
git clone https://github.com/KrishnaswamyLab/ReLSO-Guided-Generative-Protein-Design-using-Regularized-Transformers.git


# install project   
cd ReLSO-Guided-Generative-Protein-Design-using-Regularized-Transformers 
pip install -e .   
pip install -r requirements.txt

Usage

Training models

# run training script
python train_relso.py  --data gifford

*note: if arg option is not relevant to current model selection, it will not be used. See init method of each model to see what's used.

available dataset args:

    gifford, GB1_WU, GFP, TAPE

available auxnetwork args:

    base_reg

Original data sources

You might also like...
An implementation of a sequence to sequence neural network using an encoder-decoder
An implementation of a sequence to sequence neural network using an encoder-decoder

Keras implementation of a sequence to sequence model for time series prediction using an encoder-decoder architecture. I created this post to share a

Sequence lineage information extracted from RKI sequence data repo
Sequence lineage information extracted from RKI sequence data repo

Pango lineage information for German SARS-CoV-2 sequences This repository contains a join of the metadata and pango lineage tables of all German SARS-

Official repository of OFA. Paper: Unifying Architectures, Tasks, and Modalities Through a Simple Sequence-to-Sequence Learning Framework
Official repository of OFA. Paper: Unifying Architectures, Tasks, and Modalities Through a Simple Sequence-to-Sequence Learning Framework

Paper | Blog OFA is a unified multimodal pretrained model that unifies modalities (i.e., cross-modality, vision, language) and tasks (e.g., image gene

Aircraft design optimization made fast through modern automatic differentiation
Aircraft design optimization made fast through modern automatic differentiation

Aircraft design optimization made fast through modern automatic differentiation. Plug-and-play analysis tools for aerodynamics, propulsion, structures, trajectory design, and much more.

Genetic Algorithm, Particle Swarm Optimization, Simulated Annealing, Ant Colony Optimization Algorithm,Immune Algorithm, Artificial Fish Swarm Algorithm, Differential Evolution and TSP(Traveling salesman)
Genetic Algorithm, Particle Swarm Optimization, Simulated Annealing, Ant Colony Optimization Algorithm,Immune Algorithm, Artificial Fish Swarm Algorithm, Differential Evolution and TSP(Traveling salesman)

scikit-opt Swarm Intelligence in Python (Genetic Algorithm, Particle Swarm Optimization, Simulated Annealing, Ant Colony Algorithm, Immune Algorithm,A

library for nonlinear optimization, wrapping many algorithms for global and local, constrained or unconstrained, optimization

NLopt is a library for nonlinear local and global optimization, for functions with and without gradient information. It is designed as a simple, unifi

Racing line optimization algorithm in python that uses Particle Swarm Optimization.
Racing line optimization algorithm in python that uses Particle Swarm Optimization.

Racing Line Optimization with PSO This repository contains a racing line optimization algorithm in python that uses Particle Swarm Optimization. Requi

Puzzle-CAM: Improved localization via matching partial and full features.
Puzzle-CAM: Improved localization via matching partial and full features.

Puzzle-CAM The official implementation of "Puzzle-CAM: Improved localization via matching partial and full features".

[ECCVW2020] Robust Long-Term Object Tracking via Improved Discriminative Model Prediction (RLT-DiMP)
[ECCVW2020] Robust Long-Term Object Tracking via Improved Discriminative Model Prediction (RLT-DiMP)

Feel free to visit my homepage Robust Long-Term Object Tracking via Improved Discriminative Model Prediction (RLT-DIMP) [ECCVW2020 paper] Presentation

Comments
  • Conda env create not working

    Conda env create not working

    When I type in the command as instructed in how to run, I get this error:

    Warning: you have pip-installed dependencies in your environment file, but you do not list pip itself as one of your conda dependencies. Conda may not use the correct pip to install your packages, and they may end up in the wrong place. Please add an explicit pip dependency. I'm adding one for you, but still nagging you. Collecting package metadata (repodata.json): done Solving environment: failed

    ResolvePackageNotFound:

    • libcxx==12.0.0=h2f01273_0
    • python==3.10.4=hdfd78df_0
    • openssl==1.1.1q=hca72f7f_0
    • ncurses==6.3=hca72f7f_3
    • readline==8.1.2=hca72f7f_1
    • bzip2==1.0.8=h1de35cc_0
    • ca-certificates==2022.07.19=hecd8cb5_0
    • xz==5.2.5=hca72f7f_1
    • libffi==3.3=hb1e8313_2
    • zlib==1.2.12=h4dc903c_2
    • sqlite==3.38.5=h707629a_0
    • tk==8.6.12=h5d9f67b_0
    opened by Pixelatory 1
  • May the internal information of gifford data leads to a bias results given by model?

    May the internal information of gifford data leads to a bias results given by model?

    I'm very intersted in your work and analysize the gifford data. Firstly, I use the CD-HIT( a Cluster tool) split into different clusters.Then, I chose the sequence (comes the Clsuter-1(a cluster subset contaiing similar sequences given by CD-HIT)) with highest enrich value as a baseline, and focus on the residue difference between it and others sequences. Very interstingly, i find those sequences that containg 2 or 3 different residues compared to baseline sequence, usually have high enrichments. In Top-100 high enrichments, it can at 65%. As i know, your work is a multitask that both focus on generation and prediction. **I wonder that whether the JT-VAE tends to produce the new sequences that different from the corresponding baseline sequence with highest enrichment about 2 or 3 different residues , and the prediction neural network may think such sequences are good results.**It means that the model only need to realize the fact that compared to high enrich sequnces,the new sequnces contain 2 or 3 different residues is good enough. Beacuse i not find your results, i hope you can give me some advices.

    opened by chengyunzhang 0
Releases(v1.0)
Owner
Krishnaswamy Lab
Krishnaswamy Lab
Populating 3D Scenes by Learning Human-Scene Interaction https://posa.is.tue.mpg.de/

Populating 3D Scenes by Learning Human-Scene Interaction [Project Page] [Paper] License Software Copyright License for non-commercial scientific resea

Mohamed Hassan 81 Nov 08, 2022
Real-time analysis of intracranial neurophysiology recordings.

py_neuromodulation Click this button to run the "Tutorial ML with py_neuro" notebooks: The py_neuromodulation toolbox allows for real time capable pro

Interventional Cognitive Neuromodulation - Neumann Lab Berlin 15 Nov 03, 2022
A PyTorch implementation for our paper "Dual Contrastive Learning: Text Classification via Label-Aware Data Augmentation".

Dual-Contrastive-Learning A PyTorch implementation for our paper "Dual Contrastive Learning: Text Classification via Label-Aware Data Augmentation". Y

hoshi-hiyouga 85 Dec 26, 2022
Deep RGB-D Saliency Detection with Depth-Sensitive Attention and Automatic Multi-Modal Fusion (CVPR'2021, Oral)

DSA^2 F: Deep RGB-D Saliency Detection with Depth-Sensitive Attention and Automatic Multi-Modal Fusion (CVPR'2021, Oral) This repo is the official imp

如今我已剑指天涯 46 Dec 21, 2022
A simple approach to emable dense segmentation with ViT.

Vision Transformer Segmentation Network This implementation of ViT in pytorch uses a super simple and straight-forward way of generating an output of

HReynaud 5 Jan 03, 2023
catch-22: CAnonical Time-series CHaracteristics

catch22 - CAnonical Time-series CHaracteristics About catch22 is a collection of 22 time-series features coded in C that can be run from Python, R, Ma

Carl H Lubba 229 Oct 21, 2022
A large-image collection explorer and fast classification tool

IMAX: Interactive Multi-image Analysis eXplorer This is an interactive tool for visualize and classify multiple images at a time. It written in Python

Matias Carrasco Kind 23 Dec 16, 2022
tsflex - feature-extraction benchmarking

tsflex - feature-extraction benchmarking This repository withholds the benchmark results and visualization code of the tsflex paper and toolkit. Flow

PreDiCT.IDLab 5 Mar 25, 2022
Official Pytorch Implementation for Splicing ViT Features for Semantic Appearance Transfer presenting Splice

Splicing ViT Features for Semantic Appearance Transfer [Project Page] Splice is a method for semantic appearance transfer, as described in Splicing Vi

Omer Bar Tal 253 Jan 06, 2023
Code repo for "Cross-Scale Internal Graph Neural Network for Image Super-Resolution" (NeurIPS'20)

IGNN Code repo for "Cross-Scale Internal Graph Neural Network for Image Super-Resolution" [paper] [supp] Prepare datasets 1 Download training dataset

Shangchen Zhou 278 Jan 03, 2023
EdMIPS: Rethinking Differentiable Search for Mixed-Precision Neural Networks

EdMIPS is an efficient algorithm to search the optimal mixed-precision neural network directly without proxy task on ImageNet given computation budgets. It can be applied to many popular network arch

Zhaowei Cai 47 Dec 30, 2022
TensorFlow 2 implementation of the Yahoo Open-NSFW model

TensorFlow 2 implementation of the Yahoo Open-NSFW model

Bosco Yung 101 Jan 01, 2023
Datasets, Transforms and Models specific to Computer Vision

torchvision The torchvision package consists of popular datasets, model architectures, and common image transformations for computer vision. Installat

13.1k Jan 02, 2023
Volumetric parameterization of the placenta to a flattened template

placenta-flattening A MATLAB algorithm for volumetric mesh parameterization. Developed for mapping a placenta segmentation derived from an MRI image t

Mazdak Abulnaga 12 Mar 14, 2022
Data reduction pipeline for KOALA on the AAT.

KOALA KOALA, the Kilofibre Optical AAT Lenslet Array, is a wide-field, high efficiency, integral field unit used by the AAOmega spectrograph on the 3.

4 Sep 26, 2022
PyTorch implementation of our ICCV 2021 paper, Interpretation of Emergent Communication in Heterogeneous Collaborative Embodied Agents.

PyTorch implementation of our ICCV 2021 paper, Interpretation of Emergent Communication in Heterogeneous Collaborative Embodied Agents.

Saim Wani 4 May 08, 2022
HyperSeg: Patch-wise Hypernetwork for Real-time Semantic Segmentation Official PyTorch Implementation

: We present a novel, real-time, semantic segmentation network in which the encoder both encodes and generates the parameters (weights) of the decoder. Furthermore, to allow maximal adaptivity, the w

Yuval Nirkin 182 Dec 14, 2022
A Python parser that takes the content of a text file and then reads it into variables.

Text-File-Parser A Python parser that takes the content of a text file and then reads into variables. Input.text File 1. What is your ***? 1. 18 -

Kelvin 0 Jul 26, 2021
Fast algorithms to compute an approximation of the minimal volume oriented bounding box of a point cloud in 3D.

ApproxMVBB Status Build UnitTests Homepage Fast algorithms to compute an approximation of the minimal volume oriented bounding box of a point cloud in

Gabriel Nützi 390 Dec 31, 2022
PyTorch implementation for "Sharpness-aware Quantization for Deep Neural Networks".

Sharpness-aware Quantization for Deep Neural Networks This is the official repository for our paper: Sharpness-aware Quantization for Deep Neural Netw

Zhuang AI Group 30 Dec 19, 2022