This repository contains the code for Direct Molecular Conformation Generation (DMCG).

Related tags

Deep LearningDMCG
Overview

Direct Molecular Conformation Generation

This repository contains the code for Direct Molecular Conformation Generation (DMCG).

Dataset

Download rdkit_folder.tar.gz from this url.

tar -xvf rdkit_folder.tar.gz

Requirements and Installation

  • PyTorch
  • Torch-Geometric

You can build a Docker image with the Dockerfile. To install DMCG and develop it locally

pip install -e . 

Train

The first time you run this code, you should specify the data path with --base-path, and the code will binarize data into binarized format.

bash run_training.sh --dropout 0.1 --use-bn --no-3drot  \
    --aux-loss 0.2 --num-layers 6 --lr 2e-4 --batch-size 128 --vae-beta-min 0.0001 --vae-beta-max 0.03 \
    --reuse-prior --node-attn --data-split confgf --pred-pos-residual \
    --dataset-name qm9 --remove-hs --shared-output  --base-path $yourdatapath

Test

python evaluate.py --dropout 0.1 --use-bn --lr-warmup --use-adamw --train-subset \
    --num-layers 6 --eval-from  $yourcktpath --workers 20 --batch-size 128 \
    --reuse-prior --node-attn --data-split confgf --dataset-name qm9 --remove-hs \
    --shared-output --pred-pos-residual --sample-beta 1.2
Deep Learning Package based on TensorFlow

White-Box-Layer is a Python module for deep learning built on top of TensorFlow and is distributed under the MIT license. The project was started in M

YeongHyeon Park 7 Dec 27, 2021
In-place Parallel Super Scalar Samplesort (IPS⁴o)

In-place Parallel Super Scalar Samplesort (IPS⁴o) This is the implementation of the algorithm IPS⁴o presented in the paper Engineering In-place (Share

82 Dec 22, 2022
ERISHA is a mulitilingual multispeaker expressive speech synthesis framework. It can transfer the expressivity to the speaker's voice for which no expressive speech corpus is available.

ERISHA: Multilingual Multispeaker Expressive Text-to-Speech Library ERISHA is a multilingual multispeaker expressive speech synthesis framework. It ca

Ajinkya Kulkarni 43 Nov 27, 2022
A Benchmark For Measuring Systematic Generalization of Multi-Hierarchical Reasoning

Orchard Dataset This repository contains the code used for generating the Orchard Dataset, as seen in the Multi-Hierarchical Reasoning in Sequences: S

Bill Pung 1 Jun 05, 2022
Source code for the NeurIPS 2021 paper "On the Second-order Convergence Properties of Random Search Methods"

Second-order Convergence Properties of Random Search Methods This repository the paper "On the Second-order Convergence Properties of Random Search Me

Adamos Solomou 0 Nov 13, 2021
Designing a Minimal Retrieve-and-Read System for Open-Domain Question Answering (NAACL 2021)

Designing a Minimal Retrieve-and-Read System for Open-Domain Question Answering Abstract In open-domain question answering (QA), retrieve-and-read mec

Clova AI Research 34 Apr 13, 2022
Si Adek Keras is software VR dangerous object detection.

Si Adek Python Keras Sistem Informasi Deteksi Benda Berbahaya Keras Python. Version 1.0 Developed by Ananda Rauf Maududi. Developed date: 24 November

Ananda Rauf 1 Dec 21, 2021
DPT: Deformable Patch-based Transformer for Visual Recognition (ACM MM2021)

DPT This repo is the official implementation of DPT: Deformable Patch-based Transformer for Visual Recognition (ACM MM2021). We provide code and model

CASIA-IVA-Lab 111 Dec 21, 2022
Label-Free Model Evaluation with Semi-Structured Dataset Representations

Label-Free Model Evaluation with Semi-Structured Dataset Representations Prerequisites This code uses the following libraries Python 3.7 NumPy PyTorch

8 Oct 06, 2022
This repo provides the official code for TransBTS: Multimodal Brain Tumor Segmentation Using Transformer (https://arxiv.org/pdf/2103.04430.pdf).

TransBTS: Multimodal Brain Tumor Segmentation Using Transformer This repo is the official implementation for TransBTS: Multimodal Brain Tumor Segmenta

Raymond 247 Dec 28, 2022
PIGLeT: Language Grounding Through Neuro-Symbolic Interaction in a 3D World [ACL 2021]

piglet PIGLeT: Language Grounding Through Neuro-Symbolic Interaction in a 3D World [ACL 2021] This repo contains code and data for PIGLeT. If you like

Rowan Zellers 51 Oct 08, 2022
Tandem Mass Spectrum Prediction with Graph Transformers

MassFormer This is the original implementation of MassFormer, a graph transformer for small molecule MS/MS prediction. Check out the preprint on arxiv

Röst Lab 13 Oct 27, 2022
Simple Text-Generator with OpenAI gpt-2 Pytorch Implementation

GPT2-Pytorch with Text-Generator Better Language Models and Their Implications Our model, called GPT-2 (a successor to GPT), was trained simply to pre

Tae-Hwan Jung 775 Jan 08, 2023
Very large and sparse networks appear often in the wild and present unique algorithmic opportunities and challenges for the practitioner

Sparse network learning with snlpy Very large and sparse networks appear often in the wild and present unique algorithmic opportunities and challenges

Andrew Stolman 1 Apr 30, 2021
A general framework for inferring CNNs efficiently. Reduce the inference latency of MobileNet-V3 by 1.3x on an iPhone XS Max without sacrificing accuracy.

GFNet-Pytorch (NeurIPS 2020) This repo contains the official code and pre-trained models for the glance and focus network (GFNet). Glance and Focus: a

Rainforest Wang 169 Oct 28, 2022
GANmouflage: 3D Object Nondetection with Texture Fields

GANmouflage: 3D Object Nondetection with Texture Fields Rui Guo1 Jasmine Collins

29 Aug 10, 2022
TiP-Adapter: Training-free CLIP-Adapter for Better Vision-Language Modeling

TiP-Adapter: Training-free CLIP-Adapter for Better Vision-Language Modeling This is the official code release for the paper 'TiP-Adapter: Training-fre

peng gao 189 Jan 04, 2023
Code for CoMatch: Semi-supervised Learning with Contrastive Graph Regularization

CoMatch: Semi-supervised Learning with Contrastive Graph Regularization (Salesforce Research) This is a PyTorch implementation of the CoMatch paper [B

Salesforce 107 Dec 14, 2022
Pca-on-genotypes - Mini bioinformatics project - PCA on genotypes

Mini bioinformatics project: PCA on genotypes This repo contains the code from t

Maria Nattestad 8 Dec 04, 2022
TUPÃ was developed to analyze electric field properties in molecular simulations

TUPÃ: Electric field analyses for molecular simulations What is TUPÃ? TUPÃ (pronounced as tu-pan) is a python algorithm that employs MDAnalysis engine

Marcelo D. Polêto 10 Jul 17, 2022