177 Open source projects that are alternatives of or similar to FLIP

Neural Networks for Protein Sequence Alignment

Guided Conditional Wasserstein GAN for De Novo Protein Design

Protein-protein, protein-peptide and protein-DNA docking framework based on the GSO algorithm

A suite of tools to explore protein structures with Protein Blocks 🐍

Object-aware Contrastive Learning for Debiased Scene Representation (NeurIPS 2021)

Tasks Assessing Protein Embeddings (TAPE), a set of five biologically relevant semi-supervised learning tasks spread across different domains of protein biology. (DEPRECATED)

Representation learning-based graph alignment based on implicit matrix factorization and structural embeddings

waka waka

Ἀνατομή is a PyTorch library to analyze representation of neural networks

web-based protein structure viewer and analysis tool interactively or in batch mode

Template with code & dataset for the "Structural basis for solubility in protein expression systems" challenge at the Copenhagen Bioinformatics Hackathon 2021.

Inference of couplings in proteins and RNAs from sequence variation

Preforms De novo protein design using machine learning and PyRosetta to generate a novel protein structure

Implements the ideas presented in https://arxiv.org/pdf/2004.11362v1.pdf by Khosla et al.

A library for evaluating representations.

[NeurIPS 2021] COCO-LM: Correcting and Contrasting Text Sequences for Language Model Pretraining

A pytorch implementation of the paper "Prediction, Consistency, Curvature: Representation Learning for Locally-Linear Control"

Official git repository for Biopython (originally converted from CVS)

Parametric UMAP embeddings for representation and semisupervised learning. From the paper "Parametric UMAP: learning embeddings with deep neural networks for representation and semi-supervised learning" (Sainburg, McInnes, Gentner, 2020).

Evolutionary couplings from protein and RNA sequence alignments

Predictive Coding for Locally-Linear Control (ICML-2020)

Must-read papers and resources related to causal inference and machine (deep) learning

VSCode Extension for interactively visualising protein structure data in the editor

Vector Quantized Autoregressive Predictive Coding (VQ-APC)

Nucleotide Archival Format - Compressed file format for DNA/RNA/protein sequences

Modelling the Language of Life - Deep Learning Protein Sequences

Pytorch implementation of Paper by Google Research - Representation Learning for Information Extraction from Form-like Documents.

Differentiable molecular simulation of proteins with a coarse-grained potential

Paratope Prediction using Deep Learning

An attempt at the implementation of GLOM, Geoffrey Hinton's paper for emergent part-whole hierarchies from data

Graph Network for protein-protein interface

Implementation of experiments in paper "Learning from Rules Generalizing Labeled Exemplars" to appear in ICLR2020 (https://openreview.net/forum?id=SkeuexBtDr)

Winning Solution of the NeurIPS 2020 Competition on Predicting Generalization in Deep Learning

📚 🔬 PIA - Protein Inference Algorithms

🌐 Deep Embedded Self-Organizing Map: Joint Representation Learning and Self-Organization

PyTorch code for NeurIPSW 2020 paper (4th Workshop on Meta-Learning) "Few-Shot Unsupervised Continual Learning through Meta-Examples"

Recurrent Geometric Network in Pytorch

An implementation of "Community Preserving Network Embedding" (AAAI 2017)

Official code of our work, Unified Pre-training for Program Understanding and Generation [NAACL 2021].

View proteins and trajectories in the terminal

🧬 An R package for visualizing molecular data in 3D

pair2vec: Compositional Word-Pair Embeddings for Cross-Sentence Inference

A simplified drug discovery pipeline -- generating SMILE molecular with AlphaSMILES, predicting protein structure with AlphaFold, and checking the druggability with fpocket/Amber.

Using efficientnet to provide embeddings for retrieval

Protein cavity identification and automatic subpocket decomposition

What and How Well You Performed? A Multitask Learning Approach to Action Quality Assessment [CVPR 2019]

Fast and flexible ORF finder

Jupyter Dock is a set of Jupyter Notebooks for performing molecular docking protocols interactively, as well as visualizing, converting file formats and analyzing the results.

ProteinGCN: Protein model quality assessment using Graph Convolutional Networks

This repository contains the code implementation used in the paper Temporally Coherent Embeddings for Self-Supervised Video Representation Learning (TCE).

Protein structure comparison tools such as SSAP and SNAP

Methods for the parallel and distributed analysis and mining of the Protein Data Bank using MMTF and Apache Spark.

Official repository for the paper "Large-scale clinical interpretation of genetic variants using evolutionary data and deep learning". Joint collaboration between the Marks lab and the OATML group.

Bioinformatics toolkits for manipulating sequence, alignment, and phylogenetic tree files

A dependency-free cross-platform swiss army knife for PDB files.

FluentDNA allows you to browse sequence data of any size using a zooming visualization similar to Google Maps. You can use FluentDNA as a standalone program or as a python module for your own bioinformatics projects.

ProtVec can be used in protein interaction predictions, structure prediction, and protein data visualization.

Revisiting Contrastive Methods for Unsupervised Learning of Visual Representations. [NeurIPS 2021]

Tutorials for Machine Learning on Graphs

Official adversarial mixup resynthesis repository