Data-driven methods for accelerating polymer design

TK Patra - ACS Polymers Au, 2021 - ACS Publications
Optimal design of polymers is a challenging task due to their enormous chemical and
configurational space. Recent advances in computations, machine learning, and increasing …

A renaissance of neural networks in drug discovery

II Baskin, D Winkler, IV Tetko - Expert opinion on drug discovery, 2016 - Taylor & Francis
Introduction: Neural networks are becoming a very popular method for solving machine
learning and artificial intelligence problems. The variety of neural network types and their …

Deep architectures and deep learning in chemoinformatics: the prediction of aqueous solubility for drug-like molecules

A Lusci, G Pollastri, P Baldi - Journal of chemical information and …, 2013 - ACS Publications
Shallow machine learning methods have been applied to chemoinformatics problems with
some success. As more data becomes available and more complex problems are tackled …

The graph neural network model

F Scarselli, M Gori, AC Tsoi… - IEEE transactions on …, 2008 - ieeexplore.ieee.org
Many underlying relationships among data in several areas of science and engineering, eg,
computer vision, molecular chemistry, molecular biology, pattern recognition, and data …

Graph kernels for chemical informatics

L Ralaivola, SJ Swamidass, H Saigo, P Baldi - Neural networks, 2005 - Elsevier
Increased availability of large repositories of chemical compounds is creating new
challenges and opportunities for the application of machine learning methods to problems in …

HiGNN: A hierarchical informative graph neural network for molecular property prediction equipped with feature-wise attention

W Zhu, Y Zhang, D Zhao, J Xu… - Journal of Chemical …, 2022 - ACS Publications
Elucidating and accurately predicting the druggability and bioactivities of molecules plays a
pivotal role in drug design and discovery and remains an open challenge. Recently, graph …

Machine Learning Methods for Property Prediction in Chemoinformatics: Quo Vadis?

A Varnek, I Baskin - Journal of chemical information and modeling, 2012 - ACS Publications
This paper is focused on modern approaches to machine learning, most of which are as yet
used infrequently or not at all in chemoinformatics. Machine learning methods are …

[PDF][PDF] The principled design of large-scale recursive neural network architectures--dag-rnns and the protein structure prediction problem

P Baldi, G Pollastri - The Journal of Machine Learning Research, 2003 - jmlr.org
We describe a general methodology for the design of large-scale recursive neural network
architectures (DAG-RNNs) which comprises three fundamental steps:(1) representation of a …

[PDF][PDF] Kernels for small molecules and the prediction of mutagenicity, toxicity and anti-cancer activity

SJ Swamidass, J Chen, J Bruand, P Phung… - …, 2005 - cbio.ensmp.fr
Motivation: Small molecules play a fundamental role in organic chemistry and biology. They
can be used to probe biological systems and to discover new drugs and other useful …

A self-organizing map for adaptive processing of structured data

M Hagenbuchner, A Sperduti… - IEEE transactions on …, 2003 - ieeexplore.ieee.org
Recent developments in the area of neural networks produced models capable of dealing
with structured data. Here, we propose the first fully unsupervised model, namely an …